Major resources of bioinformatics 2
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Bioinformatics combines computer science, statistics, mathematics, and engineering to analyze biological data. Major bioinformatics databases and resources include NCBI, EMBL-EBI, and ExPASy. NCBI was established in 1988 as part of the National Library of Medicine and contains databases like PubMed, OMIM, and PubChem. EMBL-EBI was established in 1980 and provides DNA sequences and additional biological information through tools like Webin and SRS. ExPASy was established in 1993 by the Swiss Institute of Bioinformatics and contains protein databases like Swiss-Prot, TrEMBL, and InterPro.
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Protein data bank
The Protein Data Bank (PDB) is an open database that archives 3D structural data of biological macromolecules. It was established in 1971 and currently holds over 150,000 structures determined by X-ray crystallography or NMR spectroscopy. The PDB is overseen by the Worldwide Protein Data Bank and freely accessible online. It serves as a key resource for structural biology and many other databases rely on protein structures deposited in the PDB.
Comparative genomics
Comparative genomics involves comparing genomes to discover similarities and differences. It can provide insights into evolutionary relationships, help predict gene function, and aid in drug discovery. The first step is often aligning genome sequences using tools like BLAST or MUMmer. Genomes can then be compared at various levels, such as overall nucleotide statistics, genome structure, and coding/non-coding regions. Comparing gene and protein content across genomes helps predict functions. Conserved genomic features across species also aid prediction. Insights into genome evolution come from studying molecular events like inversions and duplications. Comparative genomics has impacted phylogenetics and drug target identification.
Swiss prot database
This presentation gives you a detailed information about the swiss prot database that comes under UniProtKB. It also covers TrEMBL: a computer annotated supplement to Swiss-Prot.
Protein Databases
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
Sequence alig Sequence Alignment Pairwise alignment:-
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
Gen bank databases
GenBank is a database that contains annotated nucleotide and protein sequences. It includes genomic DNA, mRNA, and EST sequences. There are three main sections in a GenBank file - the header, features, and sequence. The header provides definition, accession number, organism, and reference information. The features section contains gene and protein annotation. The sequence section displays the actual nucleotide or amino acid sequence. Understanding the GenBank file format helps effectively search and retrieve sequences from this important biological database.
Protein data bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
Protein Databases
Protein databases contain information on protein sequences, structures, and functions. The major protein databases are:
- Protein Data Bank (PDB) which contains 3D protein structures determined via X-ray crystallography or NMR.
- Swiss-Prot which contains manually annotated protein sequences and functions.
- TrEMBL which supplements Swiss-Prot with automatically annotated translations of DNA sequences.
Protein databases are important for comparing proteins, understanding relationships between proteins, and aiding the study of new proteins. Searching databases is often the first step in protein research.
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Protein data bank
The Protein Data Bank (PDB) is an open database that archives 3D structural data of biological macromolecules. It was established in 1971 and currently holds over 150,000 structures determined by X-ray crystallography or NMR spectroscopy. The PDB is overseen by the Worldwide Protein Data Bank and freely accessible online. It serves as a key resource for structural biology and many other databases rely on protein structures deposited in the PDB.
Comparative genomics
Comparative genomics involves comparing genomes to discover similarities and differences. It can provide insights into evolutionary relationships, help predict gene function, and aid in drug discovery. The first step is often aligning genome sequences using tools like BLAST or MUMmer. Genomes can then be compared at various levels, such as overall nucleotide statistics, genome structure, and coding/non-coding regions. Comparing gene and protein content across genomes helps predict functions. Conserved genomic features across species also aid prediction. Insights into genome evolution come from studying molecular events like inversions and duplications. Comparative genomics has impacted phylogenetics and drug target identification.
Swiss prot database
This presentation gives you a detailed information about the swiss prot database that comes under UniProtKB. It also covers TrEMBL: a computer annotated supplement to Swiss-Prot.
Protein Databases
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
Sequence alig Sequence Alignment Pairwise alignment:-
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
Gen bank databases
GenBank is a database that contains annotated nucleotide and protein sequences. It includes genomic DNA, mRNA, and EST sequences. There are three main sections in a GenBank file - the header, features, and sequence. The header provides definition, accession number, organism, and reference information. The features section contains gene and protein annotation. The sequence section displays the actual nucleotide or amino acid sequence. Understanding the GenBank file format helps effectively search and retrieve sequences from this important biological database.
Protein data bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
Protein Databases
Protein databases contain information on protein sequences, structures, and functions. The major protein databases are:
- Protein Data Bank (PDB) which contains 3D protein structures determined via X-ray crystallography or NMR.
- Swiss-Prot which contains manually annotated protein sequences and functions.
- TrEMBL which supplements Swiss-Prot with automatically annotated translations of DNA sequences.
Protein databases are important for comparing proteins, understanding relationships between proteins, and aiding the study of new proteins. Searching databases is often the first step in protein research.
Tools of bioinforformatics by kk
INTRODUCTION
DEFINITION OF BIOINFORMATICS
HISTORY
OBJECTIVES OF BIOINFORMATICS
TOOLS OF BIOINFORMATICS
BIOLOGICAL DATABASES
HOMOLOGY AND SIMILARITY TOOLS (SEQUENCE ALIGNMENT)
PROTEIN FUNCTION ANALYSIS TOOLS
STRUCTURAL ANALYSIS TOOLS
SEQUENCE MANIPULATION TOOLS
SEQUENCE ANALYSIS TOOLS
APPLICATION
CONCLUSION
REFERENCES
Kegg
The document describes several key databases within the KEGG resource, including:
- The PATHWAY database containing molecular network maps of metabolic and genetic pathways.
- The BRITE database providing hierarchical classifications of biological systems beyond what is shown in pathways.
- The LIGAND database consisting of chemical compounds, carbohydrates, reactions, and enzyme information.
KEGG aims to comprehensively capture biological knowledge through integrated databases covering genomes, pathways, diseases and drugs.
Uni prot presentation
UniProt is a comprehensive, freely accessible database that is a central repository for protein data. It is produced through collaboration between the European Bioinformatics Institute, Swiss Institute of Bioinformatics, and Protein Information Resource. UniProt contains protein sequences, functional information, evolutionary data, and details about biological processes, post-translational modifications, interactions, and subcellular locations to characterize proteins.
Entrez databases
The document discusses biological databases and retrieval systems. It provides an overview of Entrez, a retrieval system developed by NCBI that allows integrated searches across multiple biological databases. It also describes how Entrez links related data between databases, and some key features of Entrez like limits, preview/index, and history. Additionally, it summarizes specific NCBI databases accessible through Entrez like PubMed and OMIM, as well as another retrieval system called SRS maintained by EBI.
Protein information resource (PIR)
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
Major biological nucleotide databases
This document discusses major biological databases. It describes three types of biological databases: primary databases that contain original experimental data, secondary databases that contain additional derived information from primary databases, and composite databases that combine data from multiple sources. The document focuses on describing GenBank, a primary sequence database maintained by the National Center for Biotechnology Information. It provides details on how sequences are submitted to GenBank and how entries are formatted, including information contained in various fields like LOCUS, DEFINITION, and FEATURES. The document also briefly introduces the European Molecular Biology Laboratory database, EMBL, which collaborates with GenBank and DDBJ to exchange nucleotide sequence data daily.
European molecular biology laboratory (EMBL)
European Molecular Biology Laboratory (EMBL) is one of the biggest database related to bioinformatics research work.
Blast and fasta
This document discusses sequence alignment methods. It describes global and local alignment, and algorithms used for alignment including dot matrix analysis, dynamic programming, and word/k-tuple methods as implemented in FASTA and BLAST programs. BLAST and FASTA are described as popular tools for sequence database searches that use heuristic methods and word matching to quickly identify regions of local similarity.
Tools and database of NCBI
The document discusses the National Center for Biotechnology Information (NCBI). It provides background that NCBI is part of the National Library of Medicine and houses databases relevant to biotechnology and biomedicine. It describes some of NCBI's major databases, including GenBank for DNA sequences and PubMed for biomedical literature. The document also discusses the BLAST tool and provides examples of some of NCBI's databases, such as the Nucleotide, Protein, and Structural databases.
Nucleic acid database
The Nucleic Acid Database provides structural references and a search engine for DNA and RNA structures. It depicts structures through systematic design based on biological data in tools like the RNA Viewer, Base Pair Viewer, and ATLAS. It also examines structures through innovative methods like the Musical Atlas, which uses musical algorithms to represent DNA structures as instrumental songs.
NCBI National Center for Biotechnology Information
NCBI National Center for Biotechnology InformationThapar Institute of Engineering & Technology, Patiala, Punjab, India
The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic informationGenome annotation
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Est database
ESTs are short sequences of DNA that represent genes expressed in certain tissues or organisms. They provide a quick and inexpensive way for scientists to discover new genes and map their positions in genomes. ESTs represent a snapshot of genes expressed in a tissue at a given time. Sequencing the beginning or end of cDNA clones produces 5' and 3' ESTs, which can help identify genes and study gene expression and regulation.
Blast
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
DNA data bank of japan (DDBJ)
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC.
Ddbj
The DNA Data Bank of Japan (DDBJ) is a biological database located in Japan that collects and stores nucleotide sequence data. It began operations in 1986 and exchanges data daily with the European Nucleotide Archive and GenBank to form the International Nucleotide Sequence Database Collaboration (INSDC). DDBJ accepts sequence submissions from researchers worldwide and assigns unique identification numbers to published sequences to recognize intellectual property rights. It also provides search and analysis tools and supercomputing resources to support genomic research.
Fasta
FASTA is a bioinformatics tool and biological database that is used to compare amino acid sequences of proteins or nucleotide sequences of DNA. It was first described in 1985 by Lipman and Pearson. FASTA performs fast homology searches to find similarities between a query sequence and sequences in a database. While similar to BLAST, FASTA is faster for sequence comparisons. It works by identifying patches of sequence similarity that may contain gaps. Some key FASTA programs include FASTA, TFASTA, FASTS, and FASTX/Y. FASTA is useful for applications like identification of species, establishing phylogeny, DNA mapping, and understanding protein function.
Proteins databases
This document provides an overview of protein databases. It discusses the importance of protein databases for storing and analyzing protein sequence, structure, and functional data generated by modern biology. It summarizes several major public protein databases, including UniProt, NCBI RefSeq, PDB, InterPro, and Pfam, which contain protein sequences, structures, families, domains, and functional annotations. Searching and comparing sequences in these databases is an important first step in studying new proteins.
Functional proteomics, methods and tools
INTRODUCTION
HISTORY
DEFINITION
PROTEOMICS
FUNCTIONAL PROTEOMICS
PROTEOMICS SOFTWARE
PROTEOMICS ANALYSIS
TOOLS FOR PROTEOM ANALYSIS
DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS
APLLICATIONS
LIMITATIONS
CONCLUSION
PIR- Protein Information Resource
PIR- Protein Information ResourceThapar Institute of Engineering & Technology, Patiala, Punjab, India
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
EMBL-EBI
The European Bioinformatics Institute (EBI) is a center for bioinformatics research and services located in Hinxton, UK. EBI grew out of EMBL's work providing public biological databases and offers major databases on DNA, RNA, proteins, pathways, and more. EBI's website provides access to these databases as well as a variety of bioinformatics tools for sequence analysis, proteomics, microarrays, and more through different channels on their site.
Presentation on Biological database By Elufer Akram @ University Of Science ...
This document discusses biological databases. It begins by defining what a database is and describing database architecture. It then discusses several major types of biological databases including nucleotide sequence databases like GenBank, protein sequence databases like PDB, and collaborative databases. Specific databases discussed in detail include GenBank, NCBI, DDBJ, Swiss-Prot, TrEMBL, and UniProt. The document explains the purpose and contributions of these different biological databases.
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Tools of bioinforformatics by kk
INTRODUCTION
DEFINITION OF BIOINFORMATICS
HISTORY
OBJECTIVES OF BIOINFORMATICS
TOOLS OF BIOINFORMATICS
BIOLOGICAL DATABASES
HOMOLOGY AND SIMILARITY TOOLS (SEQUENCE ALIGNMENT)
PROTEIN FUNCTION ANALYSIS TOOLS
STRUCTURAL ANALYSIS TOOLS
SEQUENCE MANIPULATION TOOLS
SEQUENCE ANALYSIS TOOLS
APPLICATION
CONCLUSION
REFERENCES
Kegg
The document describes several key databases within the KEGG resource, including:
- The PATHWAY database containing molecular network maps of metabolic and genetic pathways.
- The BRITE database providing hierarchical classifications of biological systems beyond what is shown in pathways.
- The LIGAND database consisting of chemical compounds, carbohydrates, reactions, and enzyme information.
KEGG aims to comprehensively capture biological knowledge through integrated databases covering genomes, pathways, diseases and drugs.
Uni prot presentation
UniProt is a comprehensive, freely accessible database that is a central repository for protein data. It is produced through collaboration between the European Bioinformatics Institute, Swiss Institute of Bioinformatics, and Protein Information Resource. UniProt contains protein sequences, functional information, evolutionary data, and details about biological processes, post-translational modifications, interactions, and subcellular locations to characterize proteins.
Entrez databases
The document discusses biological databases and retrieval systems. It provides an overview of Entrez, a retrieval system developed by NCBI that allows integrated searches across multiple biological databases. It also describes how Entrez links related data between databases, and some key features of Entrez like limits, preview/index, and history. Additionally, it summarizes specific NCBI databases accessible through Entrez like PubMed and OMIM, as well as another retrieval system called SRS maintained by EBI.
Protein information resource (PIR)
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
Major biological nucleotide databases
This document discusses major biological databases. It describes three types of biological databases: primary databases that contain original experimental data, secondary databases that contain additional derived information from primary databases, and composite databases that combine data from multiple sources. The document focuses on describing GenBank, a primary sequence database maintained by the National Center for Biotechnology Information. It provides details on how sequences are submitted to GenBank and how entries are formatted, including information contained in various fields like LOCUS, DEFINITION, and FEATURES. The document also briefly introduces the European Molecular Biology Laboratory database, EMBL, which collaborates with GenBank and DDBJ to exchange nucleotide sequence data daily.
European molecular biology laboratory (EMBL)
European Molecular Biology Laboratory (EMBL) is one of the biggest database related to bioinformatics research work.
Blast and fasta
This document discusses sequence alignment methods. It describes global and local alignment, and algorithms used for alignment including dot matrix analysis, dynamic programming, and word/k-tuple methods as implemented in FASTA and BLAST programs. BLAST and FASTA are described as popular tools for sequence database searches that use heuristic methods and word matching to quickly identify regions of local similarity.
Tools and database of NCBI
The document discusses the National Center for Biotechnology Information (NCBI). It provides background that NCBI is part of the National Library of Medicine and houses databases relevant to biotechnology and biomedicine. It describes some of NCBI's major databases, including GenBank for DNA sequences and PubMed for biomedical literature. The document also discusses the BLAST tool and provides examples of some of NCBI's databases, such as the Nucleotide, Protein, and Structural databases.
Nucleic acid database
The Nucleic Acid Database provides structural references and a search engine for DNA and RNA structures. It depicts structures through systematic design based on biological data in tools like the RNA Viewer, Base Pair Viewer, and ATLAS. It also examines structures through innovative methods like the Musical Atlas, which uses musical algorithms to represent DNA structures as instrumental songs.
NCBI National Center for Biotechnology Information
NCBI National Center for Biotechnology InformationThapar Institute of Engineering & Technology, Patiala, Punjab, India
The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic informationGenome annotation
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Est database
ESTs are short sequences of DNA that represent genes expressed in certain tissues or organisms. They provide a quick and inexpensive way for scientists to discover new genes and map their positions in genomes. ESTs represent a snapshot of genes expressed in a tissue at a given time. Sequencing the beginning or end of cDNA clones produces 5' and 3' ESTs, which can help identify genes and study gene expression and regulation.
Blast
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
DNA data bank of japan (DDBJ)
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC.
Ddbj
The DNA Data Bank of Japan (DDBJ) is a biological database located in Japan that collects and stores nucleotide sequence data. It began operations in 1986 and exchanges data daily with the European Nucleotide Archive and GenBank to form the International Nucleotide Sequence Database Collaboration (INSDC). DDBJ accepts sequence submissions from researchers worldwide and assigns unique identification numbers to published sequences to recognize intellectual property rights. It also provides search and analysis tools and supercomputing resources to support genomic research.
Fasta
FASTA is a bioinformatics tool and biological database that is used to compare amino acid sequences of proteins or nucleotide sequences of DNA. It was first described in 1985 by Lipman and Pearson. FASTA performs fast homology searches to find similarities between a query sequence and sequences in a database. While similar to BLAST, FASTA is faster for sequence comparisons. It works by identifying patches of sequence similarity that may contain gaps. Some key FASTA programs include FASTA, TFASTA, FASTS, and FASTX/Y. FASTA is useful for applications like identification of species, establishing phylogeny, DNA mapping, and understanding protein function.
Proteins databases
This document provides an overview of protein databases. It discusses the importance of protein databases for storing and analyzing protein sequence, structure, and functional data generated by modern biology. It summarizes several major public protein databases, including UniProt, NCBI RefSeq, PDB, InterPro, and Pfam, which contain protein sequences, structures, families, domains, and functional annotations. Searching and comparing sequences in these databases is an important first step in studying new proteins.
Functional proteomics, methods and tools
INTRODUCTION
HISTORY
DEFINITION
PROTEOMICS
FUNCTIONAL PROTEOMICS
PROTEOMICS SOFTWARE
PROTEOMICS ANALYSIS
TOOLS FOR PROTEOM ANALYSIS
DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS
APLLICATIONS
LIMITATIONS
CONCLUSION
PIR- Protein Information Resource
PIR- Protein Information ResourceThapar Institute of Engineering & Technology, Patiala, Punjab, India
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
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NCBI National Center for Biotechnology Information
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EMBL-EBI
The European Bioinformatics Institute (EBI) is a center for bioinformatics research and services located in Hinxton, UK. EBI grew out of EMBL's work providing public biological databases and offers major databases on DNA, RNA, proteins, pathways, and more. EBI's website provides access to these databases as well as a variety of bioinformatics tools for sequence analysis, proteomics, microarrays, and more through different channels on their site.
Presentation on Biological database By Elufer Akram @ University Of Science ...
This document discusses biological databases. It begins by defining what a database is and describing database architecture. It then discusses several major types of biological databases including nucleotide sequence databases like GenBank, protein sequence databases like PDB, and collaborative databases. Specific databases discussed in detail include GenBank, NCBI, DDBJ, Swiss-Prot, TrEMBL, and UniProt. The document explains the purpose and contributions of these different biological databases.
PROTEIN STRUCTURE DATABANK
This document discusses several protein databases and bioinformatics tools. It describes Protein Data Bank (PDB) as a repository for 3D structural data of proteins and nucleic acids overseen by wwPDB. National Center for Biotechnology Information (NCBI) provides access to biomedical and genomic databases. BLAST is a tool that compares sequences to databases to find similar regions and calculate statistical significance of matches. Swiss-Prot, PIR, and UniProt are comprehensive protein sequence databases that include functional information derived from literature. ExPASy is a bioinformatics resource portal offering databases and tools in areas like proteomics, genomics, and systems biology.
Sequence and Structural Databases of DNA and Protein, and its significance in...
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.
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Biological databases/ programming languages/ bioinformatic tools/
Biological database
The document discusses various types of biological databases. It describes primary databases that contain original data, secondary databases that contain processed data derived from primary databases, and composite databases that collect and filter data from multiple primary databases. Examples of specific biological databases are provided, including nucleic acid databases like GenBank, protein sequence databases like Swiss-Prot, protein structure database PDB, and metabolic pathway database KEGG. Details about the purpose and features of some of these major databases like GenBank, DDBJ, EMBL, Swiss-Prot, and PDB are outlined in the document.
Biological databases
In the era of computers life sciences databases are still understated. Here is my presentation on biological databases. Complete classification of different databases.
For more presentations and work come and visit
https://www.linkedin.com/in/shradheya-r-r-gupta-54492984/
protein databases
This document lists various protein databases that can be categorized into protein sequence databases, proteomics databases, protein structure databases, secondary databases, protein model databases, and protein-protein interaction databases. Some of the major protein sequence databases included are UniProt, Swiss-Prot, Pfam, and PROSITE. The Protein Data Bank (PDB) is a central repository for 3D protein structure data. Other databases like SCOP and CATH provide structural classification of proteins. Databases such as IntAct and STRING contain information on known and predicted protein-protein interactions.
Protein Database
Lecture delivered by T. Ashok Kumar, Head, Department of Bioinformatics, Noorul Islam College of Arts and Science, Kumaracoil, Thuckalay, INDIA. UGC Sponsored National Workshop on BIOINFORMATICS AND GENOME ANALYSIS for College Teachers on August 11 & 12, 2014. Organized by Centre for Bioinformatics, Department of Zoology, NMCC.
Protein database
Bioinformatics is the application of Information technology to store, organize and analyze the vast amount of biological data which is available in the form of sequences and structures of proteins and nucleic acids. The biological information of nucleic acids is available as sequences while the data of proteins is available as sequences and structures.
A biological database is a collection of data that is organized so that its contents can easily be accessed, managed, and updated. The activity of preparing a database can be divided in to:
Collection of data in a form which can be easily accessed
Making it available to a multi-user system (always available for the user)
Primary and secondary databases ppt by puneet kulyana
This document provides an introduction to databases used for biological data. It defines key terms like data, information, and databases. It describes different types of biological databases including primary databases that contain original experimental data, and secondary databases that contain derived or analyzed data. Examples of primary databases include GenBank, EMBL, and PDB, while secondary databases include PROSITE, PRINTS, and Pfam that contain conserved protein motifs and families. The document also compares primary and secondary databases.
Primary, secondary, tertiary biological database
Introduction
Biological database
Types: 1.primary database
Nucleic acid sequence database : Genebank , EMBL, DDJB
Protein sequence database:PIR,SWISS-PROT,TrEMBL
2. Secondary database
PRINTS
PROSITE
PROFILES
BLOCKS
IDENTITY
3. Composite database: Non-redundant databases (NRDB)
Non-redundant protein sequence databases (OWL)
SWISS-PROT+ TrEMBL
MIPSX
Important database search tool
Application
UniProt
UniProt is a comprehensive database of protein sequences and functional information that is curated by the European Bioinformatics Institute, SIB Swiss Institute of Bioinformatics, and the Protein Information Resource. It contains three main components: UniProtKB for functional information, UniRef for clustered sequences, and UniParc for comprehensive protein sequences. As genome sequencing increases, UniProt provides centralized storage and interconnection of protein data from various sources to further scientific understanding of proteins.
Protein database
This document outlines the course content for a bioinformatics course covering 4 units:
Unit 1 introduces basic concepts of bioinformatics including proteins, DNA, RNA, and sequence, structure, and function.
Unit 2 covers major bioinformatics databases including those for nucleotide sequences, protein sequences, sequence motifs, protein structures, and other relevant databases.
Unit 3 discusses topics like single and pairwise sequence alignment, scoring matrices, and multiple sequence alignments.
Unit 4 covers the human genome project, gene and genomic databases, genomic data mining, and microarray techniques.
Introduction to Biological databases
Introduction to Biological databasesDr.K.RameshKumar, Assistant Professor,Vivekananda College,Tiruvedakam West, Madurai
The document discusses biological databases. It begins by defining what a database is, including that it is a collection of related data organized in a way that allows information to be retrieved easily. It then discusses different types of biological databases, including those containing nucleotide sequences, protein sequences, 3D structures, gene expression data, and metabolic pathways. The rest of the document provides details on specific biological databases like GenBank, EMBL, DDBJ, and NCBI databases including Entrez. It emphasizes that biological data is heterogeneous, large in volume, dynamic and integrated across multiple databases.European Molecular Biology Laboratory (EMBL)- European Bioinformatics Institu...
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Building the Database with International Isolates: European Molecular Biology Laboratory (EMBL)- European Bioinformatics Institute (EBI). Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Nucleic acid and protein databanks
The document discusses several key nucleic acid and protein databases. It describes the Nucleic Acid Database, which provides 3D structure information about nucleic acids. It also discusses NCBI, a collection of biomedical databases including GenBank that are freely accessible online. Other databases mentioned include EMBL, DDBJ, PDB, Swiss-Prot, and UniProt, each of which archives and provides access to nucleotide or protein sequence data.
Bioinformatics introduction
Bioinformatics is the application of computer science and information technology to biological data. It helps analyze biological data to gain understanding. Biological databases store biological information collected from experiments in an organized manner. There are primary databases containing raw experimental data and secondary databases containing analyzed data. Major types of biological databases include sequence databases for nucleic acid and protein sequences, and structural databases like PDB for 3D protein structures. Databases can be retrieved using tools like Entrez, SRS, and BLAST to find related sequences and information. Biological databases play an important role in research by acting as repositories of information.
Biological databases
This document summarizes different types of biological data and biological databases. It discusses primary databases like GenBank, EMBL and DDBJ that contain raw nucleotide sequence data. Secondary databases like KEGG and Pfam analyze and annotate primary database content. Composite databases like NCBI aggregate data from multiple primary sources. Protein databases discussed include Swiss-Prot, TrEMBL, PDB, and Pfam. Structural databases such as SCOP, CATH and PDB organize protein structures.
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Presentation on Biological database By Elufer Akram @ University Of Science ...
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Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/Equivariant neural networks and representation theory
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
Immersive Learning That Works: Research Grounding and Paths Forward
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
The debris of the ‘last major merger’ is dynamically young
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
Micronuclei test.M.sc.zoology.fisheries.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
Applied Science: Thermodynamics, Laws & Methodology.pdf
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
原版制作(carleton毕业证书)卡尔顿大学毕业证硕士文凭原版一模一样
原版纸张【微信：741003700 】【(carleton毕业证书)卡尔顿大学毕业证】【微信：741003700 】学位证，留信认证（真实可查，永久存档）offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma
1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
Cytokines and their role in immune regulation.pptx
This presentation covers the content and information on "Cytokines " and their role in immune regulation .
SAR of Medicinal Chemistry 1st by dk.pdf
In this presentation include the prototype drug SAR on thus or with their examples .
Syllabus of Second Year B. Pharmacy
2019 PATTERN.
Thornton ESPP slides UK WW Network 4_6_24.pdf
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
Compexometric titration/Chelatorphy titration/chelating titration
Classification
Metal ion ion indicators
Masking and demasking reagents
Estimation of Magnisium sulphate
Calcium gluconate
Complexometric Titration/ chelatometry titration/chelating titration, introduction, Types-
1.Direct Titration
2.Back Titration
3.Replacement Titration
4.Indirect Titration
Masking agent, Demasking agents
formation of complex
comparition between masking and demasking agents,
Indicators/Metal ion indicators/ Metallochromic indicators/pM indicators,
Visual Technique,PM indicators (metallochromic), Indicators of pH, Redox Indicators
Instrumental Techniques-Photometry
Potentiometry
Miscellaneous methods.
Complex titration with EDTA.
Shallowest Oil Discovery of Turkiye.pptx
The Petroleum System of the Çukurova Field - the Shallowest Oil Discovery of Türkiye, Adana
The binding of cosmological structures by massless topological defects
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
Recently uploaded (20)
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Equivariant neural networks and representation theory
Equivariant neural networks and representation theory
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Immersive Learning That Works: Research Grounding and Paths Forward
Immersive Learning That Works: Research Grounding and Paths Forward
The debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically young
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Applied Science: Thermodynamics, Laws & Methodology.pdf
Applied Science: Thermodynamics, Laws & Methodology.pdf
Cytokines and their role in immune regulation.pptx
Cytokines and their role in immune regulation.pptx
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
Compexometric titration/Chelatorphy titration/chelating titration
Compexometric titration/Chelatorphy titration/chelating titration
The binding of cosmological structures by massless topological defects
The binding of cosmological structures by massless topological defects
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
Major resources of bioinformatics 2
- 1. 1 SEAT NO:- 5015 Third year of 5 years integrated course of bio analytical science
- 2. Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data 2
- 3. NCBI – National centre of biotechnology institute EMBL-EBI – European Molecular Biology Laboratory EXPASY 3
- 4. National center for biotechnology information Establish in 1988 Part of NLM Series of database Goals-create public database 4
- 5. PubMed OMIM Pubchem Compound GeneBank 5
- 6. 6
- 7. Centre for research and service in bioinformatics Establish in 1980 Goals – computer database of DNA sequence Get the nucleotide sequence for query Additional information about query 7
- 8. ▶ Submission tool – webin ▶ Retrievals system – SRS (sequence retrieval system) ▶ It provides with the required nucleotide sequence ▶ Embl database provide user related information 8
- 9. 9
- 10. by the Swiss Institute of Bioinformatics (SIB) Establish in 1993 ExPASy was called ExPASy (Expert Protein Analysis Syste m) ExPASy was the first website of the life sciences. 10
- 11. 11
- 12. SWISS-PROT & TrEMBL - Protein sequence database and computer annotated supplement UniProt - (Universal Protein Resource) It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. PIR - Protein Information Resource 12
- 13. InterPro - integration of Pfam, PRINTS, PROSITE, SWISS-PROT + TrEMBL PROSITE - database of protein families and domains Pfam - alignments and hidden Markov models covering many common protein domains 13
- 14. PDB - protein 3D structure database RasMol / Protein Explorer - molecule 3D structure viewers SCOP - Structural Classification Of Proteins UCL BSM CATH classification The DALI Domain Database FSSP - fold classification based on structure- structure alignment of proteins SWISS-MODEL - homology modeling server 14
- 15. The developed system is flexible and allows intuitive creation and execution of queries for an extensive range of bioinformatics topics 15
- 16. expasy.cbr.nrc.ca/sprot www.ncbi.nlm.nih.gov/ www.ebi.ac.uk/ expasy.cbr.nrc.ca/ 16
- 17. THANK YOU 17