KEGG Pathway Database
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Questions and Answers

What is the primary function of the search feature in the KEGG Pathway database?

  • To search for specific pathways by name or category (correct)
  • To browse pathway maps
  • To integrate data from various sources
  • To access links to relevant databases

    • What is the main advantage of the KEGG Pathway database for researchers and students?

  • It provides a comprehensive database for viral genomics
  • It provides a user-friendly interface for easy navigation
  • It integrates data from various sources for viral studies
  • It offers insights into the intricate world of biosynthesis and cellular metabolism (correct)

    • What is the source of the viral genomes in the ViruSITE database?

  • Gene Ontology (GO)
  • ViralZone
  • UniProtKB
  • NCBI Reference Sequence Database (RefSeq) (correct)

    • What sets the ViruSITE database apart from other databases?

    <p>It integrates data from various resources under human supervision</p> Signup and view all the answers

    What is the purpose of the pathway maps in the KEGG Pathway database?

    <p>To view interactive pathway maps with detailed information on molecules, enzymes, and genes</p> Signup and view all the answers

    What is the primary focus of the ViruSITE database?

    <p>Viral genomics and proteomics</p> Signup and view all the answers

    What is the primary goal of gene annotation?

    <p>To analyze the sequence and predict its potential functions</p> Signup and view all the answers

    What is the benefit of gene annotation in terms of understanding biological processes and diseases?

    <p>It enables researchers to understand how genes contribute to biological processes and diseases</p> Signup and view all the answers

    What step in the gene annotation process involves identifying open reading frames (ORFs) and predicting coding regions?

    <p>Gene Prediction</p> Signup and view all the answers

    What is the purpose of accession numbers in gene annotation?

    <p>To provide a unique identifier for sequences in the database</p> Signup and view all the answers

    What is the final output of the gene annotation process?

    <p>Comprehensive gene annotations</p> Signup and view all the answers

    What is the purpose of the iterative improvement step in gene annotation?

    <p>To update and refine annotations</p> Signup and view all the answers

    What is the primary purpose of using a primary database?

    <p>To access raw, uninterpreted experimental data for further analysis or verification</p> Signup and view all the answers

    What type of database is GenBank?

    <p>Primary database</p> Signup and view all the answers

    What is the main difference between a primary database and a secondary database?

    <p>The level of interpretation and annotation of the data</p> Signup and view all the answers

    Which database is used to store 3D structures of proteins and nucleic acids?

    <p>PDB</p> Signup and view all the answers

    What is the origin of the EMBL database?

    <p>Europe</p> Signup and view all the answers

    What is the original format of GenBank's data?

    <p>Flat file format</p> Signup and view all the answers

    What is the purpose of rich annotations in a database?

    <p>To enable searching, browsing, and analysis</p> Signup and view all the answers

    What is the purpose of BankIt, Sequin, and tbl2asn tools?

    <p>To submit sequences to GenBank</p> Signup and view all the answers

    What type of data is stored in the CoreNucleotide database?

    <p>Most of the nucleotide sequences</p> Signup and view all the answers

    What is the main goal of the International Sequence Database Collaboration (INSDC)?

    <p>To coordinate with individual laboratories and other sequence databases</p> Signup and view all the answers

    What is the characteristic of GenBank files?

    <p>Readable by both humans and computers</p> Signup and view all the answers

    What is the current status of GenBank's database?

    <p>Open access</p> Signup and view all the answers

    What is the main objective of pairwise sequence alignment?

    <p>To obtain the highest possible score, indicating the degree of similarity between two sequences</p> Signup and view all the answers

    What type of sequence alignment is used to identify short conserved regions in protein or nucleotide sequences?

    <p>Local alignment</p> Signup and view all the answers

    What is the difference between global and local alignment?

    <p>Global alignment aligns the entire length of the sequences, while local alignment aligns only the regions with the highest density of matches</p> Signup and view all the answers

    What is the purpose of a scoring system in pairwise sequence alignment?

    <p>To assign positive scores to matching characters and negative scores to mismatching characters or gaps</p> Signup and view all the answers

    What type of sequence alignment involves aligning two sequences to identify the optimal pairing of the sequences?

    <p>Pairwise sequence alignment</p> Signup and view all the answers

    What is a characteristic of global alignment?

    <p>It aligns the entire length of the sequences by maximizing overall similarity</p> Signup and view all the answers

    Study Notes

    Primary Databases

    • GenBank is a repository of known nucleotide sequences with a flat file structure, readable by humans and computers.
    • GenBank files contain information such as accession numbers, gene names, phylogenetic classification, and references to published literature.
    • GenBank has transitioned from a flat file format to a more complex structure using XML and ASN.1 formats for improved manageability and data exchange.
    • GenBank is an open-access sequence database that coordinates with individual laboratories and other sequence databases like EMBL and DDBJ.
    • GenBank is an annotated collection of all nucleotide sequences available to the public.

    GenBank Structure

    • The nucleotide database is divided into three databases at NCBI: CoreNucleotide database, Expressed Sequence Tag (EST), and Genome Survey Sequence (GSS).
    • CoreNucleotide database has most of the nucleotide sequences used and encloses all nucleotide records not in EST and GSS databases.

    Submission to GenBank

    • Sequences can be submitted to GenBank using BankIt, Sequin, and tbl2asn tools.

    KEGG Pathway Database

    • The KEGG Pathway database offers features to explore biosynthesis pathways, including search function, pathway maps, and data links.
    • Pathway maps provide detailed information on molecules, enzymes, and genes involved in each step.
    • Data links access relevant databases for genes, proteins, and other molecules associated with the pathway.

    ViruSite Database

    • ViruSite is a comprehensive database designed for viral genomics, integrating information on viral genomes, genes, and proteins from various sources.
    • ViruSite incorporates all genomes from viruses, viroids, and satellites deposited in the NCBI Reference Sequence Database (RefSeq).
    • Data from numerous resources like NCBI RefSeq, UniProtKB, Gene Ontology (GO), ViralZone, and PubMed are computationally extracted and integrated under human supervision.
    • ViruSite offers an intuitive and user-friendly interface for easy navigation and exploration.

    Gene Annotation

    • Gene annotation involves analyzing the sequence and predicting its potential functions, adding valuable information to databases.
    • Benefits of gene annotation include identifying genes and their locations, predicting gene function, providing insights into gene regulation and expression, and understanding biological processes and diseases.

    Sequence Analysis Pipeline

    • The pipeline involves pre-processing, gene prediction, functional annotation, structural annotation, integration, and visualization, quality assessment, and database submission.
    • Each step involves specific tools and techniques, including quality control, sequence assembly, identifying ORFs, predicting coding regions, protein homology, domain prediction, GO annotation, and pathway mapping.

    Accession Numbers

    • Accession numbers are unique identifiers that permanently identify sequences in the database.

    Primary vs. Secondary Databases

    • Primary databases store raw, uninterpreted experimental data, while secondary databases provide a more comprehensive view of biological information with interpretations, annotations, and functionalities for exploring relationships and functions.
    • Examples of primary databases include GenBank, DDBJ, and EMBL, while secondary databases include KEGG Pathway Database and ViruSite.

    Types of Sequence Alignment

    • Pairwise sequence alignment involves aligning two sequences to identify the optimal pairing, based on a scoring system that assigns positive scores to matching characters and negative scores to mismatching characters or gaps.
    • Multiple sequence alignment involves aligning three or more sequences to identify conserved regions and reconstruct evolutionary relationships.
    • Methods of pairwise sequence alignment include dot-matrix method, dynamic programming, and word or k-tuple method.
    • Methods of multiple sequence alignment include exhaustive algorithms and heuristic algorithms.
    • Applications of sequence alignment include identifying functional regions, understanding evolutionary relationships, and predicting protein structure and function.

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    Explore the features of KEGG Pathway Database, a valuable resource for researchers and students, including search function, pathway maps, and data links.

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