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    Bioinfo Lecture 2

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    Ali Khan
    Biological databases provide an organized collection of related biological information that allows for easy and quick retrieval. The primary biological databases are nucleotide and protein sequence databases like GenBank, Swiss-Prot, and TrEMBL. GenBank is the largest publicly available nucleotide sequence database maintained by NCBI, while Swiss-Prot and TrEMBL are the major protein sequence databases maintained by the UniProt consortium. Swiss-Prot contains manually curated protein sequences while TrEMBL contains automatic annotations to cope with the large amount of sequence data.

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    Bioinfo Lecture 2

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    Ali Khan
    19 views29 pages
    Biological databases provide an organized collection of related biological information that allows for easy and quick retrieval. The primary biological databases are nucleotide and protein sequence databases like GenBank, Swiss-Prot, and TrEMBL. GenBank is the largest publicly available nucleotide sequence database maintained by NCBI, while Swiss-Prot and TrEMBL are the major protein sequence databases maintained by the UniProt consortium. Swiss-Prot contains manually curated protein sequences while TrEMBL contains automatic annotations to cope with the large amount of sequence data.

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    Biological databases provide an organized collection of related biological information that allows for easy and quick retrieval. The primary biological databases are nucleotide and protein sequence databases like GenBank, Swiss-Prot, and TrEMBL. GenBank is the largest publicly available nucleotide sequence database maintained by NCBI, while Swiss-Prot and TrEMBL are the major protein sequence databases maintained by the UniProt consortium. Swiss-Prot contains manually curated protein sequences while TrEMBL contains automatic annotations to cope with the large amount of sequence data.

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    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    19 views29 pages

    Bioinfo Lecture 2

    Uploaded by

    Ali Khan
    Biological databases provide an organized collection of related biological information that allows for easy and quick retrieval. The primary biological databases are nucleotide and protein sequence databases like GenBank, Swiss-Prot, and TrEMBL. GenBank is the largest publicly available nucleotide sequence database maintained by NCBI, while Swiss-Prot and TrEMBL are the major protein sequence databases maintained by the UniProt consortium. Swiss-Prot contains manually curated protein sequences while TrEMBL contains automatic annotations to cope with the large amount of sequence data.

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    of 29

    Biological databases

    15/2/2019
    What is a database?

    • “A database is an organized collection of


    related information”

    Database
    Components of a Biological Database
    What are the advantages of using
    databases?
    • Easy and quick retrieval of information
    • Provide backup support
    • Databases offer unique window on the past.
    • Using databases we can answer today’s
    biological questions that may have been
    determined as many as 25 years ago. How?
    Biological databases
    • Need to collect and store biological data and
    its associated knowledge into databases

    • Fundamental to the survival of science

    • Each year, Nucleic Acids Research (NAR)


    journal dedicates an entire issue on the
    available databases!
    Types of Databases
    • The nucleotide and protein sequence
    databases are primary databases

    • The information gathered from primary


    databases are summarized in secondary
    databases
    Nucleotide sequence database
    GenBank
    • Database containing publicly available sequences for
    almost 260 000 formally described species (Benson et., al,
    Nucl. Acids Res. 2013).

    • GenBank is built and distributed by the National Center for


    Biotechnology Information (NCBI)

    • Exchanges data daily with the DNA Data Bank of Japan


    (DDBJ) and European Molecular Biology Laboratory (EMBL)

    • Each entry added to the database have specific Accession


    number.
    • https://www.ncbi.nlm.nih.gov/genbank/
    Growth of Genbank
    (1982-2014)
    Why we assign accession numbers?
    • Avoid non-specific results
    – A search on “collagen” will show many collagen
    related genes (COL1A1, COL2A etc.)

    • Secondly, COL1A1 cannot distinguish between


    species
    – A search on “COL1A1” will return collagen
    sequences from all organisms
    Starting to use GenBank
    • http://www.ncbi.nlm.nih.gov/genbank/
    JX573431.1 (FASTA Format)
    Protein sequence databases

    Swiss-Prot TrEMBL PIR


    Protein sequence databases - SwissProt
    • A collection of annotated
    protein sequences

    • Operated by the Swiss


    Institute of Bioinformatics
    (SIB)

    • Manually curated by a
    specialist and verified from
    literature

    • High quality database, gold


    standard for protein
    annotation
    SIB operates ExPASy
    Automatic vs Manual Annotation
    •Automatic • Manual

    •Quick • Flexible, can deal with


    inconsistencies
    •Use unfinished sequence or
    shotgun assembly • Consult publications as well as
    databases
    •Consistent annotation
    • However… Slow

    • Need finished sequence for


    validation
    The obvious problem with manually
    annotating the database?

    Difficult to keep pace with amount of sequence


    data generated these days. Necessary to
    supplement with an automatic alternative
    Gene/Genome Annotation
    Sequence BLAST
    alignment

    Unknown Known
    GeneMark, Glimmer etc. sequence sequence

    Validation

    NCBI NR etc. Pfam, SMART etc prediction of signal peptide etc


    TrEMBL
    • Translated EMBL

    • Contains all translations of the EMBL nucleotide


    database that have not yet been verified by the
    SwissProt specialists

    • Completely automatic so less authentic source of


    information
    Protein Information Resource (PIR)
    • Originated from the Atlas of Protein
    Sequences, the first protein- sequence
    collection database.

    • Established in 1984 by the National


    Biomedical Research Foundation (NBRF) for
    identification and interpretation of protein
    sequence information.
    Universal Protein Resource (Uniprot)
    • Unites the information in three databases, Swissprot,
    TrEMBL, and PIR

    • Consists of three parts


    1. UniprotKB – based on Swissprot and TrEMBL and is a
    comprehensive directory of protein annotations

    2. Uniref – allows for fast similarity searches such as search


    for sequences that are 90% identical

    3. Uniprot Archive – collection of Uniprot sequences and


    their history
    Uniprot
    UniProt Gene search
    • A gene search
    provides a diverse set
    of information
    present in different
    databases
    Uniref
    UniProt Archive
    Database Relationship

    UniProt
    Individual
    Lab’s Swiss-
    EMBL-Bank TrEMBL PIR
    Submission Prot
    DDBJ
    GenBank

    • UniProt/Swiss-Prot
    A manually curated database and therefore of highest accuracy
    • UniProt/TrEMBL
    Automatically annotated translations of EMBL coding sequence (CDS)
    features
    • EMBL / GenBank / DDBJ
    Primary nucleotide sequence repository

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