1. Bioinformatics is the application of computational techniques to the management and analysis of biological information. It describes using computational methods to access, analyze, and interpret biological data from databases.
2. Major databases discussed include nucleic acid databases like GenBank, protein databases like Swiss-Prot, and structure databases like PDB. Secondary databases are derived from primary database information.
3. Alignment methods like BLAST and FASTA allow comparison of two or more sequences to find similarities. Phylogenetic analysis reconstructs genetic relationships between sequences.
Bioinformatics uses computers to store, organize, and analyze biological data, particularly DNA and protein sequences. Key data types include DNA, RNA, and protein sequences, as well as data from experiments like transcriptomics and proteomics. Common analyses include sequence comparisons and searches for coding regions. DNA contains genetic information encoded as sequences of nucleotides that are read from 5' to 3'. It is double-stranded and antiparallel. Genes encode proteins through transcription of DNA to mRNA and translation of mRNA to protein.
Proteomics is the study of the structure and function of proteins. It involves identifying and quantifying the proteins expressed by a genome or cell type. Key aspects of proteomics include protein separation techniques like gel electrophoresis, mass spectrometry to identify proteins, and analyzing protein interactions and post-translational modifications. While genomes provide the blueprint, proteomics helps understand the diversity of proteins expressed and how they function together to direct cellular activities. It is a promising tool for disease diagnosis by identifying protein biomarkers.
This document discusses proteomics, which is defined as the study of the structure and function of proteins in an organism. It describes some of the key techniques used in proteomics, including two-dimensional gel electrophoresis and mass spectrometry. Two-dimensional gel electrophoresis separates proteins by their isoelectric point and molecular weight, while mass spectrometry is used to identify separated proteins by mass. The document also outlines some of the complexities in proteomics as well as advantages such as biomarker identification for disease screening and diagnosis.
This document provides an overview of proteomics and protein-protein interactions. It begins with an introduction to proteomics, including its history and importance. It then discusses protein structure, including the primary, secondary, tertiary, and quaternary levels. The document outlines different types of proteomics, such as expression, structural, and functional proteomics. It also describes the various steps involved in proteome analysis, including sample preparation, separation, identification, and use of databases. The document discusses techniques for studying protein-protein interactions and provides examples like co-immunoprecipitation and yeast two-hybrid screening. Overall, the document provides a comprehensive overview of the key concepts and methods in the field of proteomics.
BioInformatics Tools -Genomics , Proteomics and metablomicsAyeshaYousaf20
This document discusses various bioinformatics tools used for genomics, proteomics, and metabolomics. It begins with an introduction to bioinformatics and defines key terms. It then describes several important databases for nucleotide and protein sequences including NCBI, GenBank, and KEGG. Important analytical tools like BLAST and Clustal are also mentioned. Subsequent chapters discuss genomics, proteomics, and metabolomics in more detail and provide examples of specific tools used for each including KNApSAcK, MetaboAnalyst, and PSI-PRED. The document aims to outline the key concepts and computational tools involved in these three areas of bioinformatics.
The mitochondrial genome is a small circular DNA located in the mitochondria of eukaryotic cells. It encodes 13 proteins, 2 rRNAs, and 22 tRNAs that are essential for cellular respiration. Mitochondria contain their own DNA and divide independently of the cell, with replication and transcription controlled by a displacement loop region. Mutations in mitochondrial DNA occur at a higher rate than nuclear DNA and can cause various disorders and impact aging.
This document discusses microbial proteomics and various proteomics techniques. It describes structural proteomics which analyzes protein structures to identify gene functions and interaction sites. Interaction proteomics analyzes protein-protein interactions to determine functions. Expression proteomics identifies proteins differentially expressed between related samples like healthy and diseased tissue. Microbial proteomics studies microorganism proteins using techniques like mass spectrometry, electrospray ionization, and matrix-assisted laser desorption-ionization. Gel-based separation techniques including 1D, 2D, and 3D gel electrophoresis are also discussed.
Bioinformatics uses computers to store, organize, and analyze biological data, particularly DNA and protein sequences. Key data types include DNA, RNA, and protein sequences, as well as data from experiments like transcriptomics and proteomics. Common analyses include sequence comparisons and searches for coding regions. DNA contains genetic information encoded as sequences of nucleotides that are read from 5' to 3'. It is double-stranded and antiparallel. Genes encode proteins through transcription of DNA to mRNA and translation of mRNA to protein.
Proteomics is the study of the structure and function of proteins. It involves identifying and quantifying the proteins expressed by a genome or cell type. Key aspects of proteomics include protein separation techniques like gel electrophoresis, mass spectrometry to identify proteins, and analyzing protein interactions and post-translational modifications. While genomes provide the blueprint, proteomics helps understand the diversity of proteins expressed and how they function together to direct cellular activities. It is a promising tool for disease diagnosis by identifying protein biomarkers.
This document discusses proteomics, which is defined as the study of the structure and function of proteins in an organism. It describes some of the key techniques used in proteomics, including two-dimensional gel electrophoresis and mass spectrometry. Two-dimensional gel electrophoresis separates proteins by their isoelectric point and molecular weight, while mass spectrometry is used to identify separated proteins by mass. The document also outlines some of the complexities in proteomics as well as advantages such as biomarker identification for disease screening and diagnosis.
This document provides an overview of proteomics and protein-protein interactions. It begins with an introduction to proteomics, including its history and importance. It then discusses protein structure, including the primary, secondary, tertiary, and quaternary levels. The document outlines different types of proteomics, such as expression, structural, and functional proteomics. It also describes the various steps involved in proteome analysis, including sample preparation, separation, identification, and use of databases. The document discusses techniques for studying protein-protein interactions and provides examples like co-immunoprecipitation and yeast two-hybrid screening. Overall, the document provides a comprehensive overview of the key concepts and methods in the field of proteomics.
BioInformatics Tools -Genomics , Proteomics and metablomicsAyeshaYousaf20
This document discusses various bioinformatics tools used for genomics, proteomics, and metabolomics. It begins with an introduction to bioinformatics and defines key terms. It then describes several important databases for nucleotide and protein sequences including NCBI, GenBank, and KEGG. Important analytical tools like BLAST and Clustal are also mentioned. Subsequent chapters discuss genomics, proteomics, and metabolomics in more detail and provide examples of specific tools used for each including KNApSAcK, MetaboAnalyst, and PSI-PRED. The document aims to outline the key concepts and computational tools involved in these three areas of bioinformatics.
The mitochondrial genome is a small circular DNA located in the mitochondria of eukaryotic cells. It encodes 13 proteins, 2 rRNAs, and 22 tRNAs that are essential for cellular respiration. Mitochondria contain their own DNA and divide independently of the cell, with replication and transcription controlled by a displacement loop region. Mutations in mitochondrial DNA occur at a higher rate than nuclear DNA and can cause various disorders and impact aging.
This document discusses microbial proteomics and various proteomics techniques. It describes structural proteomics which analyzes protein structures to identify gene functions and interaction sites. Interaction proteomics analyzes protein-protein interactions to determine functions. Expression proteomics identifies proteins differentially expressed between related samples like healthy and diseased tissue. Microbial proteomics studies microorganism proteins using techniques like mass spectrometry, electrospray ionization, and matrix-assisted laser desorption-ionization. Gel-based separation techniques including 1D, 2D, and 3D gel electrophoresis are also discussed.
DNA molecules are made up of nucleotides, which each consist of a nitrogenous base, a pentose sugar, and a phosphate group. Nucleotides are linked together through covalent bonds between the sugar and phosphate groups to form polynucleotides. The sequence of bases along the DNA polymer is unique to each gene. DNA contains the genetic instructions to direct the development, functioning and reproduction of living organisms. While only about 1.5% of human DNA actually codes for proteins, recent evidence indicates non-coding DNA also plays important roles in the cell.
As a sub-discipline of biology, cell biology is concerned with the study of the structure and function of cells. As such, it can explain the structure of different types of cells, types of cell components, the metabolic processes of a cell, cell life cycle and signaling pathways to name a few.
Here, we shall look at some of the major areas of cell biology including some of the tools used.
The document discusses protein-protein interactions (PPIs), which occur when two or more protein molecules make physical contact with each other. It describes different types of PPIs such as homo-oligomers and hetero-oligomers, as well as transient and stable interactions. Methods for studying PPIs are also examined, including experimental techniques like yeast two-hybrid systems as well as computational approaches like structure-based modeling and sequence-based prediction. Protein docking is discussed as a way to model and analyze PPIs at the atomic level.
Ribosomal RNA (rRNA) is a type of RNA that provides the structural scaffold of the ribosome. There are three main types of rRNA - 5S, 16S, and 23S rRNA - that vary in size between species but together can comprise up to 90% of a cell's total RNA. rRNA forms distinctive secondary structures and is organized into operons within genomes. Comparative sequence analysis has revealed highly conserved secondary and tertiary structures that have been largely validated by ribosome crystal structures.
Protein databases can contain either sequence or structure information. Some key protein sequence databases include PIR, Swiss-Prot, and TrEMBL. PIR classifies entries by annotation level, Swiss-Prot aims to provide high annotation levels and interlink information, and TrEMBL contains all coding sequences with some entries eventually incorporated into Swiss-Prot. Important structure databases are PDB, which contains 3D protein structures, and SCOP and CATH, which classify evolutionary and structural relationships between protein domains.
This document discusses investigating protein structure using online tools. It provides an overview of protein structure, describing how amino acid sequences fold into specific three-dimensional structures, including alpha helices, beta strands, and membrane proteins. It also mentions several online tools that can be used to analyze protein sequences and structures, such as SCOP, CATH, and tools to analyze domains, folds, interactions, and structural variations.
Protein Sequence, Structure, and Functional Databases: UniProtKB, Swiss-Prot, TrEMBL, PIR, MIPS, PROSITE, PRINTS, BLOCKS, Pfam, NDRB, OWL, PDB, SCOP, CATH, NDB, PQS, SYSTERS, and Motif. Presented at UGC Sponsored National Workshop on Bioinformatics and Sequence Analysis conducted by Nesamony Memorial Christian College, Marthandam on 9th and 10th October, 2017 by Prof. T. Ashok Kumar
This document provides an introduction to proteomics. It begins by defining proteomics as the large-scale study of proteins, their structures and functions. Unlike genomics, the proteome is constantly changing through biochemical interactions. Key points made include: proteomics aims to describe the deployment of proteins in an organism over time and space; post-translational modifications mean proteins differ from what is suggested by genes; and mass spectrometry, electrophoresis and chromatography are important technologies used to identify and characterize proteins and their interactions.
Genes contain DNA instructions that control heredity and cell functions. DNA is transcribed into RNA, which helps produce proteins through a multi-step process of transcription, RNA processing, and translation. Gene expression and protein production are regulated through genetic and enzyme mechanisms to control cell biochemistry. Cells reproduce through mitosis and differentiate during development. Cancer arises from genetic mutations that disrupt normal cell growth controls.
During her summer internship at Knome Inc., Neha Gupta worked on multiple bioinformatics projects including interpreting the effects of genetic variants using Condel scores and performing pedigree analysis and estimating inbreeding using PLINK. She wrote scripts, researched tools like MAPP, and analyzed outputs to evaluate Condel scores. Future work includes integrating additional tools into Condel scoring and automating MAPP for whole genome analysis. She gained valuable experience working independently and as part of a team on challenging projects.
This document summarizes a presentation on protein-protein interactions. It discusses biological aspects of PPIs and introduces several PPI databases and tools. The presentation is divided into sections on the introduction of PPIs, databases like BIND and DIP, pathways and algorithms, and visualization tools. It provides information on the types and methods of studying PPIs experimentally.
definition of Mitochondrial gene expression
structure of mitochondrial dna
requirment for transcriptional activity
transcription elongation and termination
post transcriptional modification
translation of mitochondrial transcripts
DNA is transcribed into mRNA which is then translated into proteins. Transcription involves RNA polymerase making an RNA complement of a DNA sequence, replacing thymine with uracil. Translation involves tRNAs bringing amino acids to ribosomes where they are linked together into polypeptides based on the mRNA code. The ribosome facilitates decoding the mRNA into a protein product.
1. DNA contains the genetic instructions used in the construction of proteins.
2. DNA is made of nucleotides containing nitrogen bases, sugars, and phosphates that form the famous double helix structure.
3. DNA is replicated to produce identical copies that are distributed to daughter cells after cell division. This ensures each new cell has the complete genetic code.
4. The DNA code is transcribed into mRNA which carries protein building instructions out of the nucleus. During translation, these mRNA instructions are used to assemble amino acids in the proper sequence specified by the genetic code to produce proteins.
TrEMBL is a computer-annotated protein sequence database created by Rolf Apweiler that contains translations of coding sequences from nucleotide databases like EMBL and GenBank as well as protein sequences from literature or submitted directly. The database provides automated classification and annotation to enrich the protein sequences.
Sequence and Structural Databases of DNA and Protein, and its significance in...SBituila
This document discusses various DNA and protein sequence and structural databases, including their history, roles, and available tools. Some of the key databases mentioned are NCBI, EMBL, DDBJ, GenBank, UniProt, and PDB. NCBI maintains large public nucleotide and protein databases and provides analysis tools. EMBL collects and distributes sequence data. PDB is a database for 3D structural data of biomolecules. Together, these databases provide essential resources for genomic and proteomic research.
Lec 12 level 3-nu (gene expression and synthesis of protein)dream10f
1. Nucleotides are the building blocks of nucleic acids DNA and RNA and are composed of a nitrogenous base, a pentose sugar, and a phosphate group.
2. DNA is a double-stranded molecule where the strands are held together by hydrogen bonds between complementary nucleotide bases. It is located in the nucleus and contains the genetic information of a cell.
3. RNA acts as a messenger to transfer genetic information from DNA to the protein synthesis machinery of the cell and exists in several types including mRNA, tRNA, and rRNA.
DNA contains the genetic code that is transcribed into messenger RNA (mRNA) which is then translated into proteins. There are three main types of RNA - mRNA carries the genetic code from DNA to the ribosome for protein production. Ribosomal RNA (rRNA) helps join mRNA to transfer RNA (tRNA) during protein synthesis. TRNA transports amino acids to the ribosome where they are linked together based on the mRNA codon sequence.
This document discusses how microarrays and RNA sequencing (RNA-Seq) are complementary approaches for genomics research. It notes that while RNA-Seq is useful for discovering unknown transcripts, microarrays allow researchers to quickly and cost-effectively profile known pathways and genes. The document also highlights how microarrays can generate data from limited or degraded RNA samples not amenable to RNA-Seq, and can validate potential RNA-Seq hits simultaneously. It concludes by emphasizing the robust, cost-effective, and proven nature of microarray technology as a complement to emerging NGS approaches.
DNA molecules are made up of nucleotides, which each consist of a nitrogenous base, a pentose sugar, and a phosphate group. Nucleotides are linked together through covalent bonds between the sugar and phosphate groups to form polynucleotides. The sequence of bases along the DNA polymer is unique to each gene. DNA contains the genetic instructions to direct the development, functioning and reproduction of living organisms. While only about 1.5% of human DNA actually codes for proteins, recent evidence indicates non-coding DNA also plays important roles in the cell.
As a sub-discipline of biology, cell biology is concerned with the study of the structure and function of cells. As such, it can explain the structure of different types of cells, types of cell components, the metabolic processes of a cell, cell life cycle and signaling pathways to name a few.
Here, we shall look at some of the major areas of cell biology including some of the tools used.
The document discusses protein-protein interactions (PPIs), which occur when two or more protein molecules make physical contact with each other. It describes different types of PPIs such as homo-oligomers and hetero-oligomers, as well as transient and stable interactions. Methods for studying PPIs are also examined, including experimental techniques like yeast two-hybrid systems as well as computational approaches like structure-based modeling and sequence-based prediction. Protein docking is discussed as a way to model and analyze PPIs at the atomic level.
Ribosomal RNA (rRNA) is a type of RNA that provides the structural scaffold of the ribosome. There are three main types of rRNA - 5S, 16S, and 23S rRNA - that vary in size between species but together can comprise up to 90% of a cell's total RNA. rRNA forms distinctive secondary structures and is organized into operons within genomes. Comparative sequence analysis has revealed highly conserved secondary and tertiary structures that have been largely validated by ribosome crystal structures.
Protein databases can contain either sequence or structure information. Some key protein sequence databases include PIR, Swiss-Prot, and TrEMBL. PIR classifies entries by annotation level, Swiss-Prot aims to provide high annotation levels and interlink information, and TrEMBL contains all coding sequences with some entries eventually incorporated into Swiss-Prot. Important structure databases are PDB, which contains 3D protein structures, and SCOP and CATH, which classify evolutionary and structural relationships between protein domains.
This document discusses investigating protein structure using online tools. It provides an overview of protein structure, describing how amino acid sequences fold into specific three-dimensional structures, including alpha helices, beta strands, and membrane proteins. It also mentions several online tools that can be used to analyze protein sequences and structures, such as SCOP, CATH, and tools to analyze domains, folds, interactions, and structural variations.
Protein Sequence, Structure, and Functional Databases: UniProtKB, Swiss-Prot, TrEMBL, PIR, MIPS, PROSITE, PRINTS, BLOCKS, Pfam, NDRB, OWL, PDB, SCOP, CATH, NDB, PQS, SYSTERS, and Motif. Presented at UGC Sponsored National Workshop on Bioinformatics and Sequence Analysis conducted by Nesamony Memorial Christian College, Marthandam on 9th and 10th October, 2017 by Prof. T. Ashok Kumar
This document provides an introduction to proteomics. It begins by defining proteomics as the large-scale study of proteins, their structures and functions. Unlike genomics, the proteome is constantly changing through biochemical interactions. Key points made include: proteomics aims to describe the deployment of proteins in an organism over time and space; post-translational modifications mean proteins differ from what is suggested by genes; and mass spectrometry, electrophoresis and chromatography are important technologies used to identify and characterize proteins and their interactions.
Genes contain DNA instructions that control heredity and cell functions. DNA is transcribed into RNA, which helps produce proteins through a multi-step process of transcription, RNA processing, and translation. Gene expression and protein production are regulated through genetic and enzyme mechanisms to control cell biochemistry. Cells reproduce through mitosis and differentiate during development. Cancer arises from genetic mutations that disrupt normal cell growth controls.
During her summer internship at Knome Inc., Neha Gupta worked on multiple bioinformatics projects including interpreting the effects of genetic variants using Condel scores and performing pedigree analysis and estimating inbreeding using PLINK. She wrote scripts, researched tools like MAPP, and analyzed outputs to evaluate Condel scores. Future work includes integrating additional tools into Condel scoring and automating MAPP for whole genome analysis. She gained valuable experience working independently and as part of a team on challenging projects.
This document summarizes a presentation on protein-protein interactions. It discusses biological aspects of PPIs and introduces several PPI databases and tools. The presentation is divided into sections on the introduction of PPIs, databases like BIND and DIP, pathways and algorithms, and visualization tools. It provides information on the types and methods of studying PPIs experimentally.
definition of Mitochondrial gene expression
structure of mitochondrial dna
requirment for transcriptional activity
transcription elongation and termination
post transcriptional modification
translation of mitochondrial transcripts
DNA is transcribed into mRNA which is then translated into proteins. Transcription involves RNA polymerase making an RNA complement of a DNA sequence, replacing thymine with uracil. Translation involves tRNAs bringing amino acids to ribosomes where they are linked together into polypeptides based on the mRNA code. The ribosome facilitates decoding the mRNA into a protein product.
1. DNA contains the genetic instructions used in the construction of proteins.
2. DNA is made of nucleotides containing nitrogen bases, sugars, and phosphates that form the famous double helix structure.
3. DNA is replicated to produce identical copies that are distributed to daughter cells after cell division. This ensures each new cell has the complete genetic code.
4. The DNA code is transcribed into mRNA which carries protein building instructions out of the nucleus. During translation, these mRNA instructions are used to assemble amino acids in the proper sequence specified by the genetic code to produce proteins.
TrEMBL is a computer-annotated protein sequence database created by Rolf Apweiler that contains translations of coding sequences from nucleotide databases like EMBL and GenBank as well as protein sequences from literature or submitted directly. The database provides automated classification and annotation to enrich the protein sequences.
Sequence and Structural Databases of DNA and Protein, and its significance in...SBituila
This document discusses various DNA and protein sequence and structural databases, including their history, roles, and available tools. Some of the key databases mentioned are NCBI, EMBL, DDBJ, GenBank, UniProt, and PDB. NCBI maintains large public nucleotide and protein databases and provides analysis tools. EMBL collects and distributes sequence data. PDB is a database for 3D structural data of biomolecules. Together, these databases provide essential resources for genomic and proteomic research.
Lec 12 level 3-nu (gene expression and synthesis of protein)dream10f
1. Nucleotides are the building blocks of nucleic acids DNA and RNA and are composed of a nitrogenous base, a pentose sugar, and a phosphate group.
2. DNA is a double-stranded molecule where the strands are held together by hydrogen bonds between complementary nucleotide bases. It is located in the nucleus and contains the genetic information of a cell.
3. RNA acts as a messenger to transfer genetic information from DNA to the protein synthesis machinery of the cell and exists in several types including mRNA, tRNA, and rRNA.
DNA contains the genetic code that is transcribed into messenger RNA (mRNA) which is then translated into proteins. There are three main types of RNA - mRNA carries the genetic code from DNA to the ribosome for protein production. Ribosomal RNA (rRNA) helps join mRNA to transfer RNA (tRNA) during protein synthesis. TRNA transports amino acids to the ribosome where they are linked together based on the mRNA codon sequence.
This document discusses how microarrays and RNA sequencing (RNA-Seq) are complementary approaches for genomics research. It notes that while RNA-Seq is useful for discovering unknown transcripts, microarrays allow researchers to quickly and cost-effectively profile known pathways and genes. The document also highlights how microarrays can generate data from limited or degraded RNA samples not amenable to RNA-Seq, and can validate potential RNA-Seq hits simultaneously. It concludes by emphasizing the robust, cost-effective, and proven nature of microarray technology as a complement to emerging NGS approaches.
The document compares gene expression and alternative splicing data from an Affymetrix microarray to real-time PCR results. It shows excellent concordance between microarray and PCR for both gene-level fold changes (R=0.96) and alternative splicing events (all events validated) when using USB VeriQuest qPCR master mixes. Eighty-four genes with a wide range of expression levels were analyzed for gene-level validation, and 15 alternative splicing events from 3 tissue types were validated for splicing accuracy.
Solutions for Personalized Medicine brochureAffymetrix
The document discusses personalized medicine and describes some of the tools and technologies used for biomarker discovery and validation to enable personalized medicine. Specifically, it discusses:
1) Affymetrix provides a portfolio of tools to detect and validate DNA and RNA biomarkers for diseases like cancer through microarrays, services, and assays that can interrogate genomes, transcriptomes, genes, pathways, and individual molecules.
2) RNA and DNA biomarkers like gene expressions levels, mutations, and other genomic alterations can serve as indicators of disease processes and therapeutic responses. Affymetrix tools allow analysis of whole genomes, transcriptomes, alternative splicing, and single-cell analysis.
3) These tools are used to discover and validate biomarkers which
Supporting high throughput high-biotechnologies in today’s research environme...Ed Dodds
The document describes the Hartwell Center at St. Jude Children's Research Hospital, which provides integrated high-throughput biotechnology services and resources to support research. The Center consolidates services like DNA sequencing, microarray analysis, proteomics, and bioinformatics. It has over 30 staff members and provides resources like automated lab equipment, databases, and high-performance computing. The Center aims to promote collaborative research through these shared resources and has impacted over 500 publications. Key elements of its success include strategic planning, leadership, career opportunities for staff, integration of technologies, scientific oversight, and consistent budget support.
Synthetic biology builds on nanotechnology and biotechnology by adding information technology to model and modify biological systems at the genetic level. It aims to program cells by reengineering genomes and integrating biology with nanotechnology. Researchers can model gene networks, validate circuits, and alter genes to design new cellular functions. The next frontier is bringing such innovations to higher organisms using stem cells. The overall goal is to understand and reprogram biology as an information processing system at the molecular scale.
The document discusses various applications and techniques of DNA microarrays, including summarizing key points about Affymetrix GeneChips, spotted microarrays, experimental design, data analysis, and several case studies on various topics like ovarian cancer, Sjogren's syndrome, wine yeast genomics, and norovirus genotyping. Microarrays allow analysis of gene expression patterns and copy number variations across genomes through comparative hybridization experiments. The document provides an overview of microarray technology and applications in genomic and biomedical research.
Comparison between RNASeq and Microarray for Gene Expression AnalysisYaoyu Wang
Transcriptome profiling using RNA-Seq or microarrays allows determination of differential gene expression between samples like normal vs. tumor. While RNA-Seq and microarrays are generally concordant, RNA-Seq provides more information like alternative splicing and novel transcripts but requires more computational resources. While the cost per sample of RNA-Seq is decreasing, storage and analysis of the large datasets requires specialized infrastructure.
The document discusses various methods in molecular biology, including nucleic acid hybridization, DNA sequencing, real-time PCR, and DNA microarrays. Nucleic acid hybridization uses complementary base pairing between DNA or RNA probes and targets. DNA sequencing determines the nucleotide order using chain-terminating dideoxynucleotides. Real-time PCR quantifies DNA or RNA targets in real time using fluorescent probes. DNA microarrays allow analysis of gene expression patterns across thousands of genes.
This document provides an overview of bioinformatics and related topics across 7 parts:
Part I introduces bioinformatics and its areas including genomics, proteomics, computational biology, and databases.
Part II discusses the history of bioinformatics from Darwin's theory of evolution to the human genome project.
Part III focuses on the human genome project, its goals of identifying genes and sequencing DNA, and its benefits like improved medicine.
Part IV explains how the internet plays an important role in bioinformatics for retrieving biological information and resources like databases, tools, and software.
Part V describes different types of biological databases including primary, secondary, and composite databases that combine different sources.
Part VI discusses knowledge discovery
Bioinformatics is the interdisciplinary study of biology and computer science. It involves developing tools to analyze large amounts of biological data, such as genetic sequences. There are two main building blocks studied in bioinformatics: nucleic acids like DNA and RNA, and proteins. DNA stores genetic information that is transcribed into RNA, which is then translated into proteins according to the genetic code. Technological advances have led to an explosion of biological data that requires bioinformatics approaches to analyze and interpret.
This document provides an overview of bioinformatics and related topics. It begins by defining bioinformatics as the use of computational techniques to understand biology. It then discusses the central dogma of biology, describing how DNA is transcribed into RNA and translated into protein. The document outlines common bioinformatics tasks like sequence analysis, databases, and modeling biological systems. It provides background on key biomolecules like DNA, RNA, and proteins and the information flow within biological systems.
1) Ribosomes use the sequence of codons in mRNA to assemble amino acids into polypeptide chains through the process of translation.
2) Messenger RNA carries codons that are read by ribosomes to direct the binding of transfer RNA molecules and the addition of amino acids to form a polypeptide chain.
3) The central dogma of molecular biology is that genetic information flows from DNA to RNA to protein, with DNA containing the genetic instructions and proteins performing most functions in cells.
DNA carries genetic information from one generation to the next and must replicate itself accurately when cells divide. DNA replication occurs via a semi-conservative process where each new DNA strand contains one original strand and one newly synthesized strand. During transcription, mRNA is synthesized from a gene on DNA using one DNA strand as a template. Translation then builds a polypeptide chain from the mRNA codon sequence using tRNA to add amino acids specified by each codon. Molecular recognition allows for specific interactions between proteins and other molecules through complementary binding of receptors, antigens, enzymes and substrates.
Chapter 20 Molecular Genetics Lesson 2 - Genes_Transcription and Translationj3di79
The document discusses how genes control the formation of proteins through transcription and translation. A gene is a segment of DNA that stores instructions to make a specific protein. During transcription, the DNA sequence is copied into messenger RNA (mRNA) in the nucleus. The mRNA then leaves the nucleus and attaches to a ribosome, where translation occurs. During translation, transfer RNA (tRNA) brings amino acids to the ribosome according to the mRNA codon sequence. This results in a polypeptide chain that folds into a protein.
Analysis of Genomic and Proteomic Sequence Using Fir FilterIJMER
Bioinformatics is a field of science that implies the use of techniques from mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Digital Signal Processing (DSP) applications in genomic sequence analysis have received great attention in recent years.DSP principles are used to analyse genomic and proteomic sequences. The DNA sequence is mapped into digital signals in the form of binary indicator sequences. Signal processing techniques such as digital filtering is applied to genomic sequences to identify protein coding region. Frequency response of genomic sequences is used to solve many optimization problems in science, medicine and many other applications. The aim of this paper is to describe a method of generating Finite Impulse Response (FIR) of the genomic sequence. The same DNA sequence is used to convert into proteomic sequence using transcription and translation, and also digital filtering technique such as FIR filter applied to know the frequency response. The frequency response is same for both gene and proteomic sequence.
Provide an in depth description of biological information transfer (.pdfMALASADHNANI
Provide an in depth description of biological information transfer (what is the chemistry
underlying each information transfer event, which nucleotide sequences are involved etc.)
Solution
The genetic information is stored in Deoxyribonucleic acid,DNA. DNA contains the information
needed to build an individual. Genetic information is transferred from DNA and converted to
protein.RNA molecules work as messengers.Proteins are the biological workers.Information of
the DNA is copied to a RNA molecule in transcription.RNA directs the protein synthesis in a
translation.Protein’s 3D structure determines it’s function.Information transfer only in one
direction.
The biological information flows from DNA to RNA,and from there to proteins.It is ultimately
the DNA that controls every function of the cell through protein synthesis.As a carrier of genetic
information,DNA in a cell must be duplicated (replicated),maintained and passed dawn
accurately to the daughter cells.
DNA is deoxyribonucleic acid,which is found in chromosomes, contains inherited
information,they are made up of nucleotides,and are what make up genes. A nucleotide is
composed of a sugar (deoxyribose),a phosphate group,and a base.There are 4 bases found in
DNA, Adenine (A),Thymine (T),Guanine (G),and Cytosine (C).Adenine and guanine are double
ring bases while thymine and cytosine are single ring bases.Nucleotides are joined to each other
by covalent bonds between the phosphate group of one nucleotide and the 3\' carbon atom of the
deoxyribose (sugar) of the next nucleotide.Each DNA molecule is unique because the order of
nucleotides is unique. The order of nucleotides determines the order of amino acids in a
protein.RNA is a nucleic acid composed of nucleotides and consists of one strand of
nucleotides.There are three different types of RNA- Ribosomal,Messenger,and
Transfer.Ribosomal RNA is the RNA molecules found in ribosomes. The large subunit RNA
contains the enzymatic activity that makes the peptide bonds between amino acids. Messenger
RNA is what controls the order of amino acids in a protein and determines which gene it codes
for.Transfer RNA brings amino acids to ribosomes.The transfer RNA has two recognition sites-
one recognizes an amino acid and the other recognizes one codon.The transfer RNA brings the
the correct amino acid to the ribosome.
Transcription is the process by which the information contained in a section of DNA is replicated
in the form of a newly assembled piece of messenger RNA (mRNA).Enzymes facilitating the
process include RNA polymerase and transcription factors.In eukaryotic cells the primary
transcript is pre-mRNA. Pre-mRNA must be processed for translation to proceed.Processing
includes the addition of a 5\' cap and a poly-A tail to the pre-mRNA chain,followed by
splicing.Alternative splicing occurs when appropriate, increasing the diversity of the proteins
that any single mRNA can produce.The product of the entire transcription process is a mature
mRNA ch.
The document discusses the genetic code and process of translation. It explains that DNA or mRNA carries the genetic code to produce proteins using codons. There are 64 possible codon combinations that code for 21 amino acids, with some codons coding for the same amino acid. Transfer RNA (tRNA) molecules contain anticodons that bind to codons and attach the corresponding amino acid. The ribosome then synthesizes proteins using the mRNA template through reading the codons and incorporating amino acids.
Transcription and translation allow genes to be expressed as proteins. Transcription involves RNA polymerase copying a gene from DNA into mRNA. Translation uses the mRNA code to assemble amino acids into a polypeptide chain via tRNA and ribosomes. The genetic code pairs 3-nucleotide codons in mRNA with specific amino acids. This allows DNA sequences to be converted into proteins through sequential transcription and translation.
1. Explain how a gene directs the synthesis of a protein. Give the l.pdfarjunanenterprises
1. Explain how a gene directs the synthesis of a protein. Give the location and a brief description
of each step of the process. Include in your explanation the words \"amino acid,\" \"anti-codon,\"
\" codon,\" \"cytoplasm,\" \"DNA,\" \"mRNA,\" \"nucleotide,\" \"nucleus,\" \"ribosome,\" \"RNA
polymerase,\" \"tRNA.\" \"transcription,\" and \"translation.\"
2. Considering that we are all made up of the same four nucleotides in our DNA, the same four
nucleotides in our RNA, and the same 20 amino acids in our proteins, why are we so different
from each other?
3. Describe what type of amino acids would be used to line the pore of a Na+ channel. Give one
example.
Solution
1. A gene directs the synthesis of a protein by a two-step process. Very first, any
recommendations inside the cistron inside the DNA can be duplicated straight into a messenger
RNA (mRNA) molecule. Any collection with nucleotides inside the cistron ascertains any
collection with nucleotides inside the mRNA. This step is named transcription. Second, any
recommendations in the messenger RNA are utilised by ribosomes towards add the most suitable
amino acids inside the fix collection to the protein coded with regard to just by which usually
gene. Any collection with nucleotides inside the mRNA ascertains any collection with amino
acids inside the protein. This step is named translation. Transcription takes area inside the
nucleus.
Transcription is any process that makes messenger RNA (mRNA), amazing begin by realizing
slightly to the structure with mRNA. mRNA is a single-stranded polymer with nucleotides, as
both versions includes nitrogenous bottom, some carbs and a phosphate team, just like the
nucleotides define DNA. mRNA is a ribonucleic chemical given that equally nucleotide in RNA
incorporates any carbs ribose, not like DNA is a deoxyribonucleic chemical given that equally
nucleotide in DNA includes another carbs, deoxyribose.
During this process of translation, any collection with nucleotides in messenger RNA (mRNA)
ascertains any collection with amino acids inside a protein. In translation, equally couple of
several nucleotides within an mRNA compound codes for around amino acid inside a protein.
This particular describes exactly why equally couple of several nucleotides inside the mRNA is
named some codon. Each codon specifies a precise amino acid. For instance, any first codon
shown over, CGU, instructs the ribosome to place the amino acid arg (arginine) because the
primary amino acid within this protein. Any collection with codons inside the mRNA ascertains
any collection with amino acids inside the protein. Any meal table beneath demonstrates any six
codons to be a part of your mRNA compound, with their amino acid numbered with regard to
just by organizations codons.
Amino acids – twenty years old substances which might be the building blocks with proteins.
Guitar string with amino acids compose protein\'s major structure.
Anticodon – some collection with several nucleot.
The document summarizes the central dogma of molecular biology, which describes the flow of genetic information from DNA to RNA to proteins. It explains the three main processes - transcription of DNA to mRNA, translation of mRNA to proteins using tRNA and ribosomes, and DNA replication. The central dogma shows how genes encoded in DNA are expressed via RNA intermediates to produce functional gene products like proteins. Some exceptions to the central dogma like reverse transcription and direct translation from DNA to proteins are also mentioned.
Genetics is the study of heredity and genetic variation. Key terms include:
- Genotype is the genetic makeup of an organism, phenotype is observable traits.
- Genes hold information to build cells and pass traits to offspring. The human genome contains 25,000-35,000 genes located on 23 chromosome pairs in the nucleus.
- DNA is transcribed to RNA and translated to proteins, which determine an organism's traits. Variations in genes and chromosomes can result in genetic disorders. Common methods to study genetics include karyotyping, analyzing pedigrees, and identifying alleles and mutations. Understanding genetics provides insight into inheritance patterns and human health.
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, constitute the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand.
Nucleic acids like DNA and RNA are long biopolymers composed of nucleotides. DNA stores genetic information in cells and is made of deoxyribonucleotides, while RNA is involved in protein synthesis and has ribonucleotides. Both are composed of nitrogenous bases, a pentose sugar, and a phosphate group. DNA exists as double-stranded helixes that are replicated for cell division. RNA exists in various forms that carry out different functions like protein synthesis.
1. Transcription is the process by which DNA is copied into messenger RNA (mRNA) by RNA polymerase. This involves three phases - initiation, elongation, and termination.
2. Eukaryotic transcription is more complex than prokaryotic transcription due to multiple RNA polymerases, nucleosomes, separation of transcription and translation, and intron-exon structure of genes.
3. Following transcription, eukaryotic mRNA undergoes processing including capping, polyadenylation, and splicing before being translated into protein by ribosomes.
This document provides an overview of RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq). It describes that RNA-Seq is used to profile transcriptomes and determine gene expression levels, while ChIP-Seq identifies the binding sites of DNA-associated proteins. The key steps of RNA-Seq are RNA preparation, library preparation, sequencing, and analysis to map reads, detect isoforms and expression levels. ChIP-Seq combines chromatin immunoprecipitation with sequencing to precisely map global binding sites of proteins of interest to understand gene regulation. Both techniques provide high-quality, genome-wide data with low input requirements compared to previous methods.
The document provides an overview of genome sequencing and related topics. It discusses:
- A brief history of genetics including key figures like Mendel and Nirenberg.
- Scientific instruments used in genome sequencing like spectrophotometers and electrophoresis instruments.
- Key terms and concepts like the genetic code, DNA, RNA, genes, and proteins.
- Characteristics of the genetic code and how it is used to synthesize proteins.
- Databases that house genome sequences like GenBank.
- Methods of sequence analysis and features that can be analyzed from DNA and protein sequences like promoters and genes.
IB Biology HL topic 7.3 Translation Presentation for the new syllabus first exams 2016. Images from the Biology Course Companion have been removed because I do not have permission to reuse them.
Protein synthesis involves transcription and translation. During transcription, DNA is copied into messenger RNA (mRNA) in the nucleus. The mRNA carries the genetic code from DNA to the cytoplasm for translation. Translation is the process by which the mRNA genetic code is used to produce a specific amino acid sequence or protein with the help of transfer RNA (tRNA) and ribosomes. The central dogma of molecular biology states that genetic information flows from DNA to RNA to protein.
• Define transcription• Define translation• What are the 3 steps.pdfarihantelehyb
• Define transcription
• Define translation
• What are the 3 steps of translation?
• Define the “genetic dogma”
• What is the function of Transfer RNA?
• What is the function of RNA polymerase?
• What is the function of DNA polymerase?
• Define “splicing of RNA”
• What is an exon?
• What component of the cell does the translation?
• What molecule in the cell does transcription?
• What are the functions of: operon, promotor?
• What is the difference between inducible operon and repressible operon?
Solution
• Define transcription
Transcription is the process of making an RNA copy of a gene sequence. This copy, called a
messenger RNA (mRNA) molecule, leaves the cell nucleus and enters the cytoplasm, where it
directs the synthesis of the protein, which it encodes. Here is a more complete definition of
transcription.
• Define translation
Translation is the process of translating the sequence of a messenger RNA (mRNA) molecule to
a sequence of amino acids during protein synthesis. The genetic code describes the relationship
between the sequence of base pairs in a gene and the corresponding amino acid sequence that it
encodes. In the cell cytoplasm, the ribosome reads the sequence of the mRNA in groups of three
bases to assemble the protein. Here is a more complete definition of translation:
• What are the 3 steps of translation?
Step # 1. Initiation:
Initiation of translation in E .coli involves the small ribosome subunit, a mRNA molecule, a
specific charge initiator tRNA, GTP, Mg++ and number of proteinaceous initiation factors (IFs).
These are initially part of the small subunit and are required to enhance binding affinity of the
various translational components (Table 8.1). Unlike ribosomal proteins, IFs are released from
the ribosome once initiation is completed.
Step # 2. Elongation:
Once both subunits of the ribosome are assembled with the mRNA, binding site for two charged
tRNA molecules are formed. These are designated as the ‘P’ or peptidyl and the ‘A’ or
aminoacyl sites. The charged initiator tRNA binds to the P site, provided that the AUG triplet of
mRNA is in the corresponding position of the small subunit. The increase of the growing
polypeptide chain by one amino acid is called elongation.
Step # 3. Termination:
Termination of protein synthesis is carried out by triplet codes (UAG, UAA, UGA; stop codons)
present at site A. These codons do not specify an amino acid, nor do they call for a tRNA in the
A site. These codons are called stop codons, termination codons or nonsense codons. The
finished polypeptide is still attached to the terminal tRNA at the P site, and the A site is empty.
• Define the “genetic dogma”
A theory in genetics and molecular biology subject to several exceptions that genetic information
is coded in self-replicating DNA and undergoes unidirectional transfer to messenger RNAs in
transcription which act as templates for protein synthesis in translation
• What is the function of Transfer RNA?
The tRNA molecule, or tr.
• Define transcription• Define translation• What are the 3 steps.pdf
916215 bioinformatics-over-view
1. Bioinformatics – An Overview
Kudipudi.Srinivas
Research Scholar, Dept of Computer Science, S.V.K.P & Dr.K.S Raju Atrs & Science College,Penugonda-534320, India
Kudipudi_sri@yahoo.com
ABSTRACT : This presentation gives an overview of Bioinformatics covering major databases
available online as well as at major research centers. The major databases called mother databases
are the nucleic acid databases and protein sequence databases. Bioinformatics has been visualized
as an interface between biological information and information technology that are employed for
Protein sequencing, DNA sequencing etc. The concept of Transcription and Translation processes
are explained by the central dogma of molecular biology, which states that the sequences of a strand
of DNA correspond to the amino acid sequence of a protein. Representation of two or more
sequences can be compared by alignment methods such as Pairwise and Multiple alignments. Some
database search tools like BLAST, FASTA are some of the programs which do intensive pairwise
alignment of our query sequence to all the database sequence entries and gives out the sequences
with best scores. Phylogenetic methods are used to reconstruct the relationships between
macromolecular sequences finding the genetic connections and relationships between species. The
paper also explains the application of bioinformatics in the various industries e.g. Food,
Pharmaceutical, Agricultural, Medical, etc., and the technologies that have enabled the analysis of
biological problems in multiple dimensions.
Keywords: Protein, DNA, FASTA, BLAST, Phylogenetic Tree, Orthologus
Introduction:
• Bioinformatics is the application of computational techniques to the management and analysis
of biological information.
• Bioinformatics describes using computational techniques to access, analyze, and interpret the
biological information in any of the available biological databases.
2. 1. DATABASES:
1.1. Primary Databases
Sequences obtained by various sequencing techniques like
• EST: Expressed Sequence Tags
• GSS: Genome Survey Sequences
• STS: Sequence Tagged Sites and
• HTG: High Throughput Sequences
have been put in different nucleic acid and protein databases, which can be accessed by the
people all over the world through World Wide Web. The major databases called mother
databases are the nucleic acid and protein sequence.
1.1.1. Nucleic Acid Databases:
The nucleic acid sequence databases consists of complete annotation of all the
nucleic acid sequences (DNA and RNA) like information of organism (source) from regions,
date on which it is sequenced etc.,
The major nucleic acid data bases are:
• European Molecular biology laboratory(EMBL)
http://www.ebi.ac.uk/
• GenBank (National center for Biotechnology Information ,NCBI)
http://www.ncbi.nlm.nih.gov/
• DNA databank of Japan (DDBJ).
http://www.ddbj.nig.ac.jp/
These are three databases under mutual collaboration facilitate the mutual exchange of data
everyday.
1.1.2. Protein Sequence Databases:
A protein sequence database consists of information of all the proteins that have been
translated from the RNA sequences and the proteins sequenced by methods like N-terminal
sequencing.
The major protein sequence databases are
• Protein Information Resource(PIR)
http://pir.georgetown.edu/
• Swiss-Prot
http://us.expasy.org/sprot/
3. 1.2. Secondary Databases:
The derived databases which are obtained by making use of the sequence information
available in the primary databases are called secondary databases. Databases like,
CUTG: Codon Usage Database of Japan
COGS: Cluster of Orthologus Groups of Protein from NCBI
PROSITE for regular expressions
PRINTS having aligned motifs and
BLOCKS having aligned motifs as blocks are fine examples of secondary databases.
1.3. Structure Databases:
The major structure databases consist of the structural data of the proteins or DNA whose
structure has been determined by either X-ray crystallography or NMR (Nuclear Magnetic
Resonance). Protein Data Bank gives details of the coordinates bond angles, torsion angles of
various proteins and nucleic acid database gives the same details about DNA and its types i.e., A-
DNA or B-DNA etc.,
Protein Data Bank (PDB)
http://www.resb.org/pdb/
The Nucleic Acid Databases (NDB)
http://ndbserver.rutgers.edu/NDB/ndb.html
Cambridge Structural Databases (CSD)
http://www.ccdc.cam.ac.uk/
These databases are an organized way to store the tremendous amount of sequence
information that accumulates from laboratories worldwide. Each database has its own specific
format. Three major database organizations around the world are responsible for maintaining most of
this data; they largely ‘mirror’ one another.
4. 2. The Central Dogma of Biology:
Central Dogma: Flow of Information
This concept is explained by the central dogma of molecular biology, which states that the
sequences of a strand of DNA correspond to the amino acid sequence of a protein.
2.1. Transcription
Transcription is the process where messenger RNA (mRNA) molecules are synthesized
from DNA molecules. Transcription takes place in the nucleus. During transcription only one of
the strands of DNA corresponding to a gene (template strand) is copied into mRNA. This mRNA
molecule will be complementary to the bases that compose the template strand. The mRNA
molecules have short lives. They travel out to the cytoplasm where they direct the synthesis of a
Protein and then they are destroyed.
5. Transcription depends on complementary base pairings. A pairs with U, U with A, C with
G and G with C. Only one of the DNA molecules is transcribed and therefore the resulting mRNA
molecule is single stranded. The amount of transcription of any given gene can be directly
controlled by the cell. Once the mRNA molecules leave the nucleus and enter the cytoplasm, they
are loaded onto the ribosome. It is at the ribosomes that protein synthesis occurs by a process
called translation. The ribosomes are composed of ribosomal RNA (rRNA) proteins and ribosomal
proteins.
2.2. Translation
Translation is the process where mRNA molecules
are translated into proteins at the ribosome. The nucleotides
of the mRNA molecule are read by the ribosome so that
each set of three nucleotides called a codon, specifies a
single amino acid. Therefore, the first three nucleotides of
the mRNA will encode the first amino acid, the second three
bases the second amino acid and so on. The rules by which
the base sequence of the mRNA molecule is translated into
the primary amino acid sequence of a protein are called the genetic code.
There are 64 different possible codons (this is because there are 4 bases: A, U, C, G, and
each codon has 3 bases, so 43 = 64) and 20 amino acids. Some codons code for more than one
amino acid and therefore the genetic code is said to be degenerate. No codon codes for more
than one amino acid.
Three of the codons do not specify the incorporation of any amino acids. These are known
as the stop codons - UAA, UAG and UGA. They are found at the end of the mRNA coding
sequence and they tell the ribosome to stop translating the message and release the protein. The
mRNA is translated from the 5' end and read one codon at a time to the 3' end. Translation
usually starts at a start codon (AUG) which codes for methionine.
Each successive codon is read and the amino acid incorporated into the protein chain until
a stop codon is encountered. The codons in a mRNA molecule do not directly recognize the
amino acids that must be incorporated. Instead this process is directed by a group of adapter
proteins called transfer RNAs (tRNAs). Every codon, except the stop codons, has its own tRNA
molecule. A tRNA molecule has an anti-codon end, which is made of a set of three base pairs.
These base pairs can base pair with the complementary codon in the mRNA. The 3' end of a
6. tRNA molecule is attached to an amino acid. In the translation process, a ribosome reads a
mRNA molecule codon by codon.
At each codon, a tRNA molecule with an anti-codon complementary to that codon attaches
to the mRNA. It brings with it the appropriate amino acid that is then incorporated into the growing
polypeptide chain. Once the amino acid has been added, the tRNA molecule is released and the
ribosome moves onto reading the next codon in the mRNA chain. This process continues until the
ribosome reads a stop codon. At this point the ribosome releases the mRNA molecule and the
completed protein. The tRNA molecule functions as an interpreter reading codons in the mRNA
molecule and translating them into amino acids. In this way, the sequence of base pairs in a given
gene determines the amino acid sequence of the protein.
3. Alignment:
Representation of two or more protein or nucleotide sequences where homologous amino
acids or nucleotides are in the same columns while missing amino acids or nucleotides replaced with
gaps.
3.1. Pair wise Alignment:
Pairwise alignment, in which only two sequences are compared. Two sequences can be
compared either by global alignment or local alignment. In global alignment the sequences are
stretched over the entire length to get the maximum number of matches and minimum number of
gaps. In local alignment, the alignment is restricted or stopped at the region, which is having the
number of matches of similarity. Local alignment uses Smith and Waterman algorithms and
Global alignment uses Needleman and Wunsch algorithms. The best alignment is chosen by the
alignment having maximum score, which is obtained for matches and negative scores for gaps
and mismatches.
Pairwise alignment is used to find the function of unknown genes or proteins by finding similar
sequences of known function. Comparing the unknown sequence with that of the whole nucleic
acid or protein databases does this. Some database search tools like BLAST, FASTA are some of
the programs which do intensive pairwise alignment of our query sequence to all the database
sequence entries and gives out the sequences with best scores.
7. 3.2. Multiple Alignment :
Multiple alignment , in which more than two sequences are compared, is used for finding
conserved regions among gene sequences and protein sequences, to study phylogenetic
relationship of macromolecular sequences i.e., to find evolutionarily related organisms. The major
multiple alignment software are clustalW, clustalX and Tcofee.
ClustalW: It is a general purpose multiple sequence alignments program for DNA or proteins
sequences. It gives biologically meaningful multiple sequence alignments of divergent sequences
and calculates the best match for the selected sequences, and lines them up so that the identities,
similarities and differences can be seen. Cladograms or Phylograms obtained is used to see the
evolutionary relationships between species. This can be either downloaded are used online at
http://www.ebi.ac.uk/clustalW/. ClustalX is the X-window based user-friendly version of clustalW,
which can be downloaded and used locally on our machine. Tcofee is more accurate than clustalW
for sequences with less than 30% identity, but it is slower.
http://www.ch.embnet.org/software/TCoffee.html
Basic Local Alignment Search Tool (BLAST):
BLAST is the heuristic search algorithm for sequence similarity searching – for example to
identify homologs to a query sequence. If a particular sequence is submitted to BLAST program, it
searches with the whole database sequences of users’ choice and in the result produces those
sequences that are showing percent identity of more than a particular threshold value. The
threshold value is set depending on user choice.
BLASTing Protein sequences:
BLASTing protein sequences is what we want to do if we already have a protein sequence
and we want to find other similar protein sequences in a sequence database. Two flavors of
BLAST that exist and deal with proteins are
blastp : Compares a protein sequence with a protein database.
tblastn : Compares a protein sequence with a nucleotide database.
FASTA:
FASTA is the first widely used program for database similarity searching. For nucleotide
searches, FastA may be more sensitive than BLAST. FastA can be very specific when identifying
long regions of low similarity especially for highly diverged sequences. FastA submission form
can be obtained at http://www.ebi.ac.uk/fasta33/
8. 4. Phylogenetic Analysis:
Phylogenetic methods are used to reconstruct the relationships between macromolecular
sequences finding the genetic connections and relationships between species. The results of
phylogenetic analysis may be depicted as a hierarchical branching diagram, a ‘cladogram’ or
‘phylogenetic tree’. Programs for Phylogenetic analysis are available at
http://evolution.genetics.washington.edu/phylip.html. This software can be downloaded free of cost
and used locally or it can be used online at http://bioportal.bic.nus.edu.sg/phylip/. Tree view and
phylodraw are the major user – friendly software to show the hierarchical clustering in different
formats used for publishing and easy analyzing. Other than this phylip software there are other
software like PAUP, Mega, TreeconW and Winboot popular for phylogenetic analysis.
5. Applications of Bioinformatics
5.1. Food Industry:
Functional genomics is playing a major role in food biotechnology industry. The complete
genome sequence information available in different databases generates information that can be
used for finding metabolic pathways, various digestive enzymes, improving cell factories and
development of novel presentation methods. The information about the various microbes, which
assist in food digestion like E.coli, also plays a vital role in the major achievements of the food
industry using Bioinformatics.
5.2. Agriculture:
Crops are improved by producing plants that have disease resistant genes to pathogens
like fungui and bacteria. Homology searches, finding conserved motifs, and molecular modeling is
useful in identifying disease resistant genes. Pesticides and insecticides that can efficiently kill the
pathogens and pests are designed by molecular modeling.
5.3. Pharmaceutical industry and Medical science:
Bioinformatics, computational biology and cheminformatics are playing a key role in
pharmaceutical industry to design new drug targets from genomic data at a very faster rate.
Disease causing genes are identified using the tools of genomics and proteomics. Drug lead
identification and drug optimization became easy using the tools of genomics and proteomics. Not
only drugs, pharmaceutical industry is using the sequence information in the production of
vaccines and therapeutic proteins. The processes of designing a new drug using bioinformatics
9. tools has been of great help in identifying Target Disease, interesting lead compounds, and by
docking studies finding the effective interaction between the drug and the compound.
Pharmacoinformatics is the area of Medical Informatics concerned with modeling and
simulation of the behavior of drugs, and control of such behavior by individualized dosage
regimens for each patient to achieve explicitly chosen therapeutic goals. The credibility of serum
concentration data is a major factor in such modeling.
Medical informatics is a scientific discipline, which is concerned with the systematic
processing of data, information and knowledge in medicine and health care. Computerization of
the patient record is expected to resolve long – standing problems with the current paper – based
system.
6. Bioinformatics in India
In India there are various research and development units, centers and sub centers,
pharmaceuticals industries doing research on various aspects of bioinformatics like proteomics,
genomics, developing sequence analysis tools, molecular modeling, drug designing etc. Department
of Biotechnology(DBT), New Delhi have emphasized on starting Bioinformatics centers with the help
of BTISnet (Biotechnology Information System) for the proper application of Bioinformatics in various
sectors of science and technology for the benefit of researchers. DBT has sponsored various
Bioinformatics Distributed Information Centers (DICs) and Distributed Information sub Centers (Sub –
DICs) all over India.
The list of the DICs and the Sub DICs can be seen in the following websites.
http://dbtindia.nic.in/btis/dic.html
http://dbtindia.nic.in/bits/subdic.html
References:
1. Bioinformatics – A Beginner’s Guide by Jean - Michel Claverie, PhD & Cedric Notredame, PhD
2. Introduction to Bioinformatics by Arthu