The document provides an introduction to the field of bioinformatics, including definitions, history, applications and key concepts. It discusses how bioinformatics uses computer algorithms and databases to analyze biological data like genomes, proteins and genes. Major databases that store DNA sequences include GenBank, EMBL and DDBJ. Other databases like PDB contain 3D protein structures. Key applications of bioinformatics include molecular biology, drug design, agriculture and clinical medicine.
The document provides an introduction to the field of bioinformatics, including definitions, history, applications and key concepts. It discusses how bioinformatics uses computer algorithms and databases to analyze biological data like genomes, proteins and genes. Major databases that store DNA sequences are described, such as GenBank, EMBL and DDBJ. Tools for analyzing sequences like BLAST are also introduced.
Role of Bioinformatics in Plant Pathology.pptxHasanRiaz18
Bioinformatics plays an important role in plant pathology and disease management. It helps with (1) studying host-pathogen interactions by identifying effector and resistance proteins, (2) studying disease genetics through techniques like linkage analysis to find susceptibility genes, (3) developing resistant cultivars by accessing gene pools and manipulating resistance genes, and (4) producing disease-free planting materials using DNA markers. Key bioinformatics tools include databases to store sequence data, BLAST for sequence alignment, and other software for tasks like genome assembly and analysis of host-pathogen interactions at the molecular level.
Bioinformatics involves gathering, storing, analyzing, and spreading vast amounts of biological data using computers and statistics. It draws from biology, computer science, and mathematics. Key areas include molecular biology, genetics, biotechnology, medicine, agriculture, and ecology. Bioinformatics addresses problems like data collection, sequence alignment, and prediction/classification. It has grown exponentially with investments and plays a role in many fields. The central dogma of molecular biology describes how genetic information flows from DNA to RNA to protein. Genomes contain genes made of DNA that code for RNA and proteins through the genetic code. A brief history outlined early biological databases and methods like sequence alignment and analysis.
This document discusses the collaboration between molecular medicine and bioinformatics. It defines bioinformatics as the science of storing, retrieving, and analyzing large amounts of biological data, cutting across biology, computer science, and mathematics. It gives examples of how bioinformatics can be applied in molecular medicine for studying pathogenicity, therapeutic targets, molecular diagnostics, and host-pathogen interactions. The document also outlines how bioinformatics supports molecular medicine through genome analysis, database and tool development, and describes some catalysts like genome sequencing that have expanded bioinformatics.
Bioinformatics for beginners (exam point of view)Sijo A
. The term bioinformatics is coined by…………………………….
Paulien Hogeweg
2. What is an entry in database?
The process of entering data into a computerised database or spreadsheet.
3. Define BLASTp
BLAST- Basic Local Alignment Search Tool
It is a homology and similarity search tool.
It is provided by NCBI.
It is used to compare a query DNA sequence with a database of sequences.
4. What is Ecogenes?
Ecogene is a database and website and it is developed to improve structural and functional annotation of E.coli K-12 MG 1655.
Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology
The document provides an introduction to the field of bioinformatics, including definitions, history, applications and key concepts. It discusses how bioinformatics uses computer algorithms and databases to analyze biological data like genomes, proteins and genes. Major databases that store DNA sequences include GenBank, EMBL and DDBJ. Other databases like PDB contain 3D protein structures. Key applications of bioinformatics include molecular biology, drug design, agriculture and clinical medicine.
The document provides an introduction to the field of bioinformatics, including definitions, history, applications and key concepts. It discusses how bioinformatics uses computer algorithms and databases to analyze biological data like genomes, proteins and genes. Major databases that store DNA sequences are described, such as GenBank, EMBL and DDBJ. Tools for analyzing sequences like BLAST are also introduced.
Role of Bioinformatics in Plant Pathology.pptxHasanRiaz18
Bioinformatics plays an important role in plant pathology and disease management. It helps with (1) studying host-pathogen interactions by identifying effector and resistance proteins, (2) studying disease genetics through techniques like linkage analysis to find susceptibility genes, (3) developing resistant cultivars by accessing gene pools and manipulating resistance genes, and (4) producing disease-free planting materials using DNA markers. Key bioinformatics tools include databases to store sequence data, BLAST for sequence alignment, and other software for tasks like genome assembly and analysis of host-pathogen interactions at the molecular level.
Bioinformatics involves gathering, storing, analyzing, and spreading vast amounts of biological data using computers and statistics. It draws from biology, computer science, and mathematics. Key areas include molecular biology, genetics, biotechnology, medicine, agriculture, and ecology. Bioinformatics addresses problems like data collection, sequence alignment, and prediction/classification. It has grown exponentially with investments and plays a role in many fields. The central dogma of molecular biology describes how genetic information flows from DNA to RNA to protein. Genomes contain genes made of DNA that code for RNA and proteins through the genetic code. A brief history outlined early biological databases and methods like sequence alignment and analysis.
This document discusses the collaboration between molecular medicine and bioinformatics. It defines bioinformatics as the science of storing, retrieving, and analyzing large amounts of biological data, cutting across biology, computer science, and mathematics. It gives examples of how bioinformatics can be applied in molecular medicine for studying pathogenicity, therapeutic targets, molecular diagnostics, and host-pathogen interactions. The document also outlines how bioinformatics supports molecular medicine through genome analysis, database and tool development, and describes some catalysts like genome sequencing that have expanded bioinformatics.
Bioinformatics for beginners (exam point of view)Sijo A
. The term bioinformatics is coined by…………………………….
Paulien Hogeweg
2. What is an entry in database?
The process of entering data into a computerised database or spreadsheet.
3. Define BLASTp
BLAST- Basic Local Alignment Search Tool
It is a homology and similarity search tool.
It is provided by NCBI.
It is used to compare a query DNA sequence with a database of sequences.
4. What is Ecogenes?
Ecogene is a database and website and it is developed to improve structural and functional annotation of E.coli K-12 MG 1655.
Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology
This document provides an introduction to biological databases and bioinformatics tools. It defines biological sequences and databases, and describes the types of bioinformatics databases including primary, secondary, and composite databases. Examples of specific biological databases like GenBank, EMBL, and SwissProt are outlined. Common bioinformatics tools for sequence analysis, structural analysis, protein function analysis, and homology/similarity searches are listed, including BLAST, FASTA, EMBOSS, ClustalW, and RasMol. Finally, important bioinformatics resources on the web are highlighted.
Bioinformatics is an interdisciplinary field that uses computational tools to analyze and manage biological data such as genes, genomes, proteins, and medical information. It involves developing mathematical models to understand relationships in complex biological systems. Key areas include analyzing protein and gene sequences, structures, and functions; understanding evolution and molecular interactions; and developing "virtual cells" through integrated modeling. Major challenges include integrating heterogeneous biological data sources and developing robust computational methods.
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
The document discusses the National Center for Biotechnology Information (NCBI), which maintains biological databases and provides bioinformatics tools. NCBI houses both primary databases directly submitted by researchers and secondary databases compiled from primary sources. Major databases include GenBank (nucleotide sequences), PubMed Central (biomedical literature), and reference sequence databases. Tools like BLAST, Entrez, and ORFfinder allow users to search and analyze sequence data. NCBI aims to make biomedical research data freely accessible worldwide.
This document provides an introduction to bioinformatics and biological databases. It defines bioinformatics as the use of computers to analyze biological data like DNA sequences. The aims of bioinformatics include developing databases of all biological information and software for tasks like drug design. Biological databases store complex biological data and can be primary databases containing raw sequences/structures or secondary databases containing derived data. Examples of primary databases include GenBank, EMBL, Swiss-Prot and PDB, while secondary databases include motif, domain, gene expression and metabolic pathway databases. Maintaining accurate, up-to-date biological databases is important for biological research and applications.
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics
The National Center for Biotechnology Information (NCBI) maintains biological databases including GenBank, which is the primary sequence database. NCBI provides tools for sequence analysis and retrieval including BLAST for sequence similarity searches. Sequence data is submitted through tools like BankIt and Sequin and added to primary databases like GenBank. NCBI databases also include literature, proteins, gene expression, structures, and chemicals.
Bioinformatics is an interdisciplinary field involving biology, computer science, mathematics and statistics. It addresses large-scale biological problems from a computational perspective. Common problems include modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution typically involves collecting statistics from biological data, building a computational model, solving a computational problem, and testing the algorithm. Bioinformatics plays a role in areas like structural genomics, functional genomics and nutritional genomics. It is used for applications such as transcriptome analysis, drug discovery, cheminformatics analysis, and more. It is an important tool in fields like molecular medicine, gene therapy, microbial genome applications, antibiotic resistance, and evolutionary studies. Biological databases are important for organizing
introduction,history scope and applications of
relation to other fields , bioinformatics,biological databases,computers internet,sequence development, and
introduction to sequence development and alignment
WHAT IS BIOINFORMATICS?
Computational Biology/Bioinformatics is the application of computer sciences and allied technologies to answer the questions of Biologists, about the mysteries of life. It has evolved to serve as the bridge between:
Observations (data) in diverse biologically-related disciplines and
The derivations of understanding (information)
APPLICATIONS OF BIOINFORMATICS
Computer Aided Drug Design
Microarray Bioinformatics
Proteomics
Genomics
Biological Databases
Phylogenetics
Systems Biology
Bioinformatics is the application of information technology to store, organize, and analyze vast amounts of biological data. It involves using mathematics, statistics, and computer science to understand and organize the information associated with biological macromolecules like DNA, RNA, and proteins. The goals of bioinformatics include uncovering biological information hidden in genetic sequences and using it to better understand areas like molecular medicine, drug development, and evolution. It utilizes tools like databases, algorithms, and data analysis to solve complex biological problems.
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.
Quantifying the content of biomedical semantic resources as a core for drug d...Syed Muhammad Ali Hasnain
The biomedical research community is providing large-scale data sources to enable knowledge discovery from the data alone, or from novel scientific experiments in combination with the existing knowledge.
Increasingly semantic Web technologies are being developed and used including ontologies, triple stores and combinations thereof.
The amount of data is constantly increasing as well as the complexity of data.
Since the data sources are publicly available, the amount of content can be derived giving an overview on the accessible content but also on the state of the data representation in comparison to the existing content.
For a better understanding of the existing data resources, i.e.\ judgments on the distribution of data triples across concepts, data types and primary providers, we have performed a comprehensive analysis which delivers an overview on the accessible content for semantic Web solutions.
It can be derived that the information related to genes, proteins and chemical entities form the center, whereas the content related to diseases and pathways forms a smaller portion.
Further data relates to dietary content and specific questions such as cancer prevention and toxicological effects of drugs.
This document provides an overview of bioinformatics. It begins by explaining how bioinformatics emerged from the need to analyze vast amounts of genetic sequence data produced by projects like the Human Genome Project. It then defines bioinformatics as the field that develops tools and methods for understanding biological data by combining computer science, statistics, and other disciplines. The document outlines several goals and applications of bioinformatics, such as identifying genes and their functions, modeling protein structures, comparing genomes, and its uses in medicine, microbial research, and more. It also provides a brief history of important developments in bioinformatics and DNA sequencing.
Bioinformatics Introduction and Use of BLAST ToolJesminBinti
Hi, I am Jesmin, studying MCSE. I think this file will help you if you want to know the basic information about Bioinformatics and the use of BLAST tool. The BLAST tool is the tool that matches the sequences of DNA,RNA and proteins.
Bioinformatics is the combination of biology and information technology used to understand biological phenomena. It involves using computational tools and methods to manage, analyze, and manipulate large amounts of biological data. Specifically, bioinformatics is concerned with applying quantitative analytical techniques to model and solve problems involving biological systems at the molecular level. It first emerged in the 1990s and deals with managing and analyzing DNA, RNA, and protein sequence data as well as other biological data like gene expression profiles, protein structures, protein interactions, microarrays, and functional analyses of biomolecules.
This document introduces bioinformatics and discusses some of its key concepts and applications. It defines bioinformatics as an interdisciplinary field that combines computer science, statistics and engineering to study and process biological data. It describes some basic cell components like DNA, RNA and proteins, and how genetics and the genetic code work. It also provides a brief history of bioinformatics, highlighting projects like the Human Genome Project. Finally, it outlines several applications of bioinformatics like phylogenetic analysis, drug design, microarray analysis and protein-protein interaction networks.
Bioinformatics is the application of computational tools and techniques to analyze and interpret biological data. It involves the development of these tools and databases, as well as their application to better understand biological systems and functions at the molecular level through analysis of genetic sequences, protein structures, and more. The goal is to gain a global understanding of cellular functions by analyzing genetic data as dictated by the central dogma of biology, and relating sequence information to protein functions and cellular processes.
Here are some suggestions for open online bioinformatics lectures and courses from famous universities:
- MIT OpenCourseWare has free bioinformatics course materials and videos from MIT courses.
- edX has massive open online courses (MOOCs) in bioinformatics from universities like Harvard, Berkeley, MIT. Some are free to audit.
- Coursera has bioinformatics courses from top universities like Johns Hopkins, University of Toronto, Peking University.
- YouTube has full lecture videos from bioinformatics courses at universities like Stanford, UC San Diego, University of Cambridge.
- Khan Academy has introductory bioinformatics lectures on topics like sequence alignment, gene finding, protein structure.
- EMBL-
This document provides an introduction to biological databases and bioinformatics tools. It defines biological sequences and databases, and describes the types of bioinformatics databases including primary, secondary, and composite databases. Examples of specific biological databases like GenBank, EMBL, and SwissProt are outlined. Common bioinformatics tools for sequence analysis, structural analysis, protein function analysis, and homology/similarity searches are listed, including BLAST, FASTA, EMBOSS, ClustalW, and RasMol. Finally, important bioinformatics resources on the web are highlighted.
Bioinformatics is an interdisciplinary field that uses computational tools to analyze and manage biological data such as genes, genomes, proteins, and medical information. It involves developing mathematical models to understand relationships in complex biological systems. Key areas include analyzing protein and gene sequences, structures, and functions; understanding evolution and molecular interactions; and developing "virtual cells" through integrated modeling. Major challenges include integrating heterogeneous biological data sources and developing robust computational methods.
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
The document discusses the National Center for Biotechnology Information (NCBI), which maintains biological databases and provides bioinformatics tools. NCBI houses both primary databases directly submitted by researchers and secondary databases compiled from primary sources. Major databases include GenBank (nucleotide sequences), PubMed Central (biomedical literature), and reference sequence databases. Tools like BLAST, Entrez, and ORFfinder allow users to search and analyze sequence data. NCBI aims to make biomedical research data freely accessible worldwide.
This document provides an introduction to bioinformatics and biological databases. It defines bioinformatics as the use of computers to analyze biological data like DNA sequences. The aims of bioinformatics include developing databases of all biological information and software for tasks like drug design. Biological databases store complex biological data and can be primary databases containing raw sequences/structures or secondary databases containing derived data. Examples of primary databases include GenBank, EMBL, Swiss-Prot and PDB, while secondary databases include motif, domain, gene expression and metabolic pathway databases. Maintaining accurate, up-to-date biological databases is important for biological research and applications.
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics
The National Center for Biotechnology Information (NCBI) maintains biological databases including GenBank, which is the primary sequence database. NCBI provides tools for sequence analysis and retrieval including BLAST for sequence similarity searches. Sequence data is submitted through tools like BankIt and Sequin and added to primary databases like GenBank. NCBI databases also include literature, proteins, gene expression, structures, and chemicals.
Bioinformatics is an interdisciplinary field involving biology, computer science, mathematics and statistics. It addresses large-scale biological problems from a computational perspective. Common problems include modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution typically involves collecting statistics from biological data, building a computational model, solving a computational problem, and testing the algorithm. Bioinformatics plays a role in areas like structural genomics, functional genomics and nutritional genomics. It is used for applications such as transcriptome analysis, drug discovery, cheminformatics analysis, and more. It is an important tool in fields like molecular medicine, gene therapy, microbial genome applications, antibiotic resistance, and evolutionary studies. Biological databases are important for organizing
introduction,history scope and applications of
relation to other fields , bioinformatics,biological databases,computers internet,sequence development, and
introduction to sequence development and alignment
WHAT IS BIOINFORMATICS?
Computational Biology/Bioinformatics is the application of computer sciences and allied technologies to answer the questions of Biologists, about the mysteries of life. It has evolved to serve as the bridge between:
Observations (data) in diverse biologically-related disciplines and
The derivations of understanding (information)
APPLICATIONS OF BIOINFORMATICS
Computer Aided Drug Design
Microarray Bioinformatics
Proteomics
Genomics
Biological Databases
Phylogenetics
Systems Biology
Bioinformatics is the application of information technology to store, organize, and analyze vast amounts of biological data. It involves using mathematics, statistics, and computer science to understand and organize the information associated with biological macromolecules like DNA, RNA, and proteins. The goals of bioinformatics include uncovering biological information hidden in genetic sequences and using it to better understand areas like molecular medicine, drug development, and evolution. It utilizes tools like databases, algorithms, and data analysis to solve complex biological problems.
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.
Quantifying the content of biomedical semantic resources as a core for drug d...Syed Muhammad Ali Hasnain
The biomedical research community is providing large-scale data sources to enable knowledge discovery from the data alone, or from novel scientific experiments in combination with the existing knowledge.
Increasingly semantic Web technologies are being developed and used including ontologies, triple stores and combinations thereof.
The amount of data is constantly increasing as well as the complexity of data.
Since the data sources are publicly available, the amount of content can be derived giving an overview on the accessible content but also on the state of the data representation in comparison to the existing content.
For a better understanding of the existing data resources, i.e.\ judgments on the distribution of data triples across concepts, data types and primary providers, we have performed a comprehensive analysis which delivers an overview on the accessible content for semantic Web solutions.
It can be derived that the information related to genes, proteins and chemical entities form the center, whereas the content related to diseases and pathways forms a smaller portion.
Further data relates to dietary content and specific questions such as cancer prevention and toxicological effects of drugs.
This document provides an overview of bioinformatics. It begins by explaining how bioinformatics emerged from the need to analyze vast amounts of genetic sequence data produced by projects like the Human Genome Project. It then defines bioinformatics as the field that develops tools and methods for understanding biological data by combining computer science, statistics, and other disciplines. The document outlines several goals and applications of bioinformatics, such as identifying genes and their functions, modeling protein structures, comparing genomes, and its uses in medicine, microbial research, and more. It also provides a brief history of important developments in bioinformatics and DNA sequencing.
Bioinformatics Introduction and Use of BLAST ToolJesminBinti
Hi, I am Jesmin, studying MCSE. I think this file will help you if you want to know the basic information about Bioinformatics and the use of BLAST tool. The BLAST tool is the tool that matches the sequences of DNA,RNA and proteins.
Bioinformatics is the combination of biology and information technology used to understand biological phenomena. It involves using computational tools and methods to manage, analyze, and manipulate large amounts of biological data. Specifically, bioinformatics is concerned with applying quantitative analytical techniques to model and solve problems involving biological systems at the molecular level. It first emerged in the 1990s and deals with managing and analyzing DNA, RNA, and protein sequence data as well as other biological data like gene expression profiles, protein structures, protein interactions, microarrays, and functional analyses of biomolecules.
This document introduces bioinformatics and discusses some of its key concepts and applications. It defines bioinformatics as an interdisciplinary field that combines computer science, statistics and engineering to study and process biological data. It describes some basic cell components like DNA, RNA and proteins, and how genetics and the genetic code work. It also provides a brief history of bioinformatics, highlighting projects like the Human Genome Project. Finally, it outlines several applications of bioinformatics like phylogenetic analysis, drug design, microarray analysis and protein-protein interaction networks.
Bioinformatics is the application of computational tools and techniques to analyze and interpret biological data. It involves the development of these tools and databases, as well as their application to better understand biological systems and functions at the molecular level through analysis of genetic sequences, protein structures, and more. The goal is to gain a global understanding of cellular functions by analyzing genetic data as dictated by the central dogma of biology, and relating sequence information to protein functions and cellular processes.
Here are some suggestions for open online bioinformatics lectures and courses from famous universities:
- MIT OpenCourseWare has free bioinformatics course materials and videos from MIT courses.
- edX has massive open online courses (MOOCs) in bioinformatics from universities like Harvard, Berkeley, MIT. Some are free to audit.
- Coursera has bioinformatics courses from top universities like Johns Hopkins, University of Toronto, Peking University.
- YouTube has full lecture videos from bioinformatics courses at universities like Stanford, UC San Diego, University of Cambridge.
- Khan Academy has introductory bioinformatics lectures on topics like sequence alignment, gene finding, protein structure.
- EMBL-
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As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
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ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
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The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Immersive Learning That Works: Research Grounding and Paths ForwardLeonel Morgado
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.
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.
3. Bioinformatics is an interdisciplinary field
that develops methods and software tools
for understanding biological data
3
4. History
• The first protein was sequenced (1955)
• Margaret O.Dayhoff
• Atlas of Protein Sequence and Structure (1965)
• Paulien Hogeweg and Ben Hesper coined “bioinformatics” in 1970
• The protein data bank (1973)
• DNA sequencing (1977)
• NCBI( 1988)
• Human genome project lunched (1990)
• The human genome is published (2001) https://www.smithsonianmag.com/science-
nature/how-margaret-dayhoff-helped-bring-
computing-scientific-research-180971904/
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7. Unites Of Information In Biological Macromolecules
DNA
Sequence analysis
Mutation and polymorphism studies
Identification of regulatory regions
Gene finding
Genome annotation
Comparative genomics
RNA
RNA sequencing
Splice variants
Tissue expression level
MicroArray
Single gene analysis
Sequence contigs
Protein
Homology modeling
Structure function prediction
Ligand docking
Protein-protein interaction
Protein expression
Phylogenic analysis 7
9. Develop templates to develop potent drug molecules
• Structural analysis of secretory phospholipase A2 from Clonorchis sinensis
https://link.springer.com/article/10.1007/s00894-011-1333-8
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19. Tumor antigens
• The ideal antigen for a cancer vaccine should be highly immunogenic,
explicitly expressed in all cancer cells (not in normal cells) and
necessary for the survival of cancer cells
• Tumor-associated antigens (TAAs)
• Tumor-specific antigens (TSAs)
20.
21.
22. Bioinformatics journals
• Briefings in Bioinformatics
• Bioinformatics
• Genomics, Proteomics & Bioinformatics
• Current Bioinformatics
• BMC Bioinformatics
• Computers in Biology and Medicine
• Journal of Computer-Aided Molecular Design
• In Silico Biology
• Journal of molecular modeling
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26. Gene
• A searchable database of genes, focusing on genomes that have been
completely sequenced and that have an active research community to
contribute gene-specific data. Information includes nomenclature,
chromosomal localization, gene products and their attributes (e.g.,
protein interactions), associated markers, phenotypes, interactions,
and links to citations, sequences, variation details, maps, expression
reports, homologs, protein domain content, and external databases
26
28. Genome
• Contains sequence and map data from the whole genomes of over
1000 organisms. The genomes represent both completely sequenced
organisms and those for which sequencing is in progress. All three
main domains of life (bacteria, archaea, and eukaryota) are
represented, as well as many viruses, phages, viroids, plasmids, and
organelles.
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30. Nucleotide
• A collection of nucleotide sequences from several sources, including
GenBank, RefSeq, the Third Party Annotation (TPA) database, and
PDB. Searching the Nucleotide Database will yield available results
from each of its component databases.
30
32. RefSeq: NCBI Reference Sequence Database
• A comprehensive, integrated, non-redundant, well-annotated set of
reference sequences including genomic, transcript, and protein.
32
33. What is the difference between RefSeq and GenBank?
• GenBank sequence records are owned by the original submitter and
cannot be altered by a third party. RefSeq sequences are not part of
the INSDC but are derived from INSDC sequences to provide non-
redundant curated data representing our current knowledge of
known genes
33
34. BLAST
• The Basic Local Alignment Search Tool (BLAST) finds regions of local
similarity between sequences. The program compares nucleotide or
protein sequences to sequence databases and calculates the statistical
significance of matches. BLAST can be used to infer functional and
evolutionary relationships between sequences as well as help identify
members of gene families.
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36. Protein
• The Protein database is a collection of sequences from several sources,
including translations from annotated coding regions in GenBank,
RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
Protein sequences are the fundamental determinants of biological
structure and function.
36
37. UniProt
• Universal Protein Resource (UniProt) is a comprehensive resource for
protein sequence and annotation data. The UniProt databases are the
UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters
(UniRef), and the UniProt Archive (UniParc). UniProt is a collaboration
between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss
Institute of Bioinformatics and the Protein Information Resource (PIR).
37
41. Protein Data Bank (PDB)
• The Protein Data Bank (PDB) is a database for the three-dimensional
structural data of large biological molecules, such as proteins and
nucleic acids.
41
The active site of the enzyme shows
the classical features of PLA2 with the participation of the
three residues: histidine-aspartic acid-tyrosine in hydrogen
bond formation. This is an interesting variation from the
house keeping group III PLA2 enzyme of human which has
a histidine-aspartic acid and phenylalanine arrangement at
the active site. This difference is therefore an important
structural parameter that can be exploited to design specific
inhibitor molecules against the pathogen PLA2
In this study, a detailed structural
and ligand binding analysis of the isoforms has been done
by modeling. The overall three dimensional structures of
the isoforms are well conserved with three helices and a bwing
stabilized by four disulfide bonds. There are characteristic
differences at the calcium binding loop, hydrophobic
channel and the C-terminal domain that can
potentially be exploited for drug binding. But the most
significant feature pertains to the catalytic site where the
isoforms exhibit three variations of either a histidineaspartate-
tyrosine or histidine-glutamate-tyrosine or histidine-
aspartate-phenylalanine. Molecular docking studies
show that isoform specific residues and their conformations
in the substrate binding hydrophobic channel make unique
interactions with certain inhibitor molecules resulting in a
perfect tight fit.
Fluorescence-based differential in-gel expression coupled with mass spectrometric analysis was used
for discovery phase of experiments, and real-time polymerase chain reaction, Western blotting, and pathway analysis were performed for expression and
functional validation of differentially expressed proteins. While aldehyde reductase, hnRNP, cyclophilin A, heat shock protein-27, and actin are upregulated
in responders, prohibitin, enoyl-coA hydratase, peroxiredoxin, and fibrin- are upregulated in the nonresponders. The expressions of some of these
proteins correlated with increased apoptotic activity in responders and decreased apoptotic activity in nonresponders. Therefore, the proteins qualify as
potential biomarkers to predict chemotherapy response.
These differences include: (1) loop-L3 between H2 and H3, which bears residue Gly80 in the wild type, is in a closed conformation with respect to the channel opening, while in the mutant enzyme it adopts a relatively open conformation; (2) the mutant enzyme is less compact and has higher solvent accessible surface area; and (3) interfacial binding contact surface area is greater, and the quality of interactions with the receptor is better in the mutant enzyme as compared to the wild type. Therefore, the structural differences delineated in this study are potential biophysical factors that could determine the increased potency of the mutant enzyme with macrophage receptor for cytokine secreting function, resulting in exacerbation of cachexia in COPD.
The gentamicin molecule binds to the lectin site of the calreticulin and lies in the concave channel formed by the long beta sheets. It makes interactions with residues Tyr109, Asp125, Asp135, Asp317 and Trp319 which are crucial for the chaperone function of the calreticulin. The superimposing of the modeled complex with the only available crystal structure complex of calreticulin with a tetrasaccharide (Glc1Man3) shows interesting features. First, the rings of the gentamicin occupy the positions of glucose and the first two mannose sugars of the tetrasaccharide molecule. Second, the oxygen atoms of the glycosidic linkage of these two ligands have a positional deviation of 1.3 Ǻ
TAAs include “self-antigens” such as differentiated antigens, overexpressed antigens, cancer-testicular antigens, and viral-original “non-self” antigens
International Nucleotide Sequence Database Collaboration (INSDC)