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Sequence Databases

Sequence Databases. June 23, 2003

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Sequence Databases

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  1. Sequence Databases • June 23, 2003 • Learning objectives-Understand how information is stored in GenBank. Learn how to read a GenBank flat file. Learn how to search GenBank for information. Understand difference between header, features and sequence. Distinguish between a primary database and secondary database.

  2. BIOSEQs • Biological sequence-central element in the NCBI data model. • Comprises a single continuous molecule of nucleic acid or protein. • Must have at least one sequence identifier (Seq-id) • Information on physical type of molecule (DNA, RNA or protein) • Annotations-refers to specific locations within the Bioseq • Descriptors-describe entire Bioseq

  3. What is GenBank? • Gene sequence database • Annotated records that represent single contiguous stretches of DNA or RNA-may have more than one coding region (limit 350 kb) • Generated from direct submissions to the DNA sequence databases from the authors. • Part of the International Nucleotide Sequence Database Collaboration.

  4. Exchange of information on a daily basis GenBank (NCBI) EMBL (EBI) United Kingdom DDBJ Japan

  5. History of GenBank • Language-ASN.1 (Abstract Syntax Notation 1)- • Began with Atlas of Protein Sequences and Structures (Dayhoff et al., 1965) • In 1986 it joined EMBL and in 1987 it joined DDBJ. • It is a primary database-Experimental data is placed into it. • Examples of secondary databases derived from GenBank/EMBL/DDBJ: Swiss-Prot, PRI. • GenBank Flat File is a human readable form of the records.

  6. General Comments on GBFF • Three sections: • 1) Header-information about the whole record • 2) Features-description of annotations-each represented by a key. • 3) Nucleotide sequence-each ends with // on last line of record. • DNA-centered • Translated sequence is a feature

  7. Feature Keys • Purpose: • 1) Indicates biological nature of sequence • 2) Supplies information about changes to sequences • Feature KeyDescription conflict Separate deter’s of the same seq. differ rep_origin Origin of replication protein_bind Protein binding site on DNA CDS Protein coding sequence

  8. Feature Keys-Terminology Feature Key Location/Qualifiers CDS 23..400 /product=“alcohol dehydro.” /gene=“adhI” The feature CDS is a coding sequence beginning at base 23 and ending at base 400, has a product called “alcohol dehydrogenase” and corresponds to the gene called “adhI”.

  9. Feature Keys-Terminology (Cont.) Feat. Key Location/Qualifiers CDS join (544..589,688..1032) /product=“T-cell recep. B-ch.” /partial The feature CDS is a partial coding sequence formed by joining the indicated elements to form one contiguous sequence encoding a product called T-cell receptor beta-chain.

  10. Record from GenBank GenBank division (plant, fungal and algal) Locus name Modification date LOCUS SCU49845 5028 bp DNA PLN 21-JUN-1999 DEFINITION Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p (AXL2) and Rev7p (REV7) genes, complete cds. ACCESSION U49845 VERSION U49845.1 GI:1293613 KEYWORDS . SOURCE baker's yeast. ORGANISM Saccharomyces cerevisiae Eukaryota; Fungi; Ascomycota; Hemiascomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces. Unique identifier (never changes) Coding region GeneInfo identifier (changes whenever there is a change) Nucleotide sequence identifier (changes when there is a change in sequence (accession.version)) Word or phrase describing the sequence (not based on controlled vocabulary). Not used in newer records. Common name for organism Formal scientific name for the source organism and its lineage based on NCBI Taxonomy Database

  11. Record from GenBank (cont.1) Oldest reference first REFERENCE 1 (bases 1 to 5028) AUTHORS Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W. TITLE Cloning and sequence of REV7, a gene whose function is required for DNA damage-induced mutagenesis in Saccharomyces cerevisiae JOURNAL Yeast 10 (11), 1503-1509 (1994) MEDLINE 95176709 REFERENCE 2 (bases 1 to 5028) AUTHORS Roemer,T., Madden,K., Chang,J. and Snyder,M. TITLE Selection of axial growth sites in yeast requires Axl2p, a novel plasma membrane glycoprotein JOURNAL Genes Dev. 10 (7), 777-793 (1996) MEDLINE 96194260 Medline UID REFERENCE 3 (bases 1 to 5028) AUTHORS Roemer,T. TITLE Direct Submission JOURNAL Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, New Haven, CT, USA Submitter of sequence (always the last reference)

  12. Record from GenBank (cont.2) There are three parts to the feature key: a keyword (indicates functional group), a location (instruction for finding the feature), and a qualifier (auxiliary information about a feature) FEATURES Location/Qualifiers source 1..5028 /organism="Saccharomyces cerevisiae" /db_xref="taxon:4932" /chromosome="IX" /map="9" CDS <1..206 /codon_start=3 /product="TCP1-beta" /protein_id="AAA98665.1" /db_xref="GI:1293614" /translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA AEVLLRVDNIIRARPRTANRQHM" Location Keys Qualifiers Partial sequence on the 5’ end. The 3’ end is complete. Start of open reading frame Descriptive free text must be in quotations Database cross-refs Protein sequence ID # Values Note: only a partial sequence

  13. Record from GenBank (cont.3) Another location gene687..3158 /gene="AXL2" CDS 687..3158 /gene="AXL2" /note="plasma membrane glycoprotein" /codon_start=1 /function="required for axial budding pattern of S. cerevisiae" /product="Axl2p" /protein_id="AAA98666.1" /db_xref="GI:1293615" /translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVN. . . “ gene complement(3300..4037) /gene="REV7" CDS complement(3300..4037) /gene="REV7" /codon_start=1 /product="Rev7p" /protein_id="AAA98667.1" /db_xref="GI:1293616" /translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ . . . “ Cutoff Another location Cutoff

  14. Record from GenBank (cont.4) BASE COUNT 1510 a 1074 c 835 g 1609 t ORIGIN 1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg 61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct . . .//

  15. EBI Sequence Retreival System SRS-author SRS-accession number SRS-title SRS-reference SRS-organism EMBL Parts of the record are parsed into separate database files

  16. Example of ASN.1 formatted text Seq-entry ::= set { level 1 , class nuc-prot , descr { title "Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p (AXL2) and Rev7p (REV7) genes, and translated products" , source { org { taxname "Saccharomyces cerevisiae" , db { { db "taxon" , tag id 4932 } } ,

  17. Primary databases vs. Secondary databases • Primary database has information from experimenter. It is called an archival database • Secondary database derives information from primary database. It is a curated datebase

  18. GenBank/EMBL/DDBJ Alu-alu repeats in human DNA dbEST-expressed sequence tags-single pass cDNA sequences (high error freq.) It is non-redundant HTGS-high-throughput genomic sequence database (errors!) PDB-Three-dimensional structure coordinates of biological molecules PROSITE-database of protein domain/function relationships. Types of primary databases carrying biological infomation

  19. dbSTS-Non-redundant db of sequence-tagged sites (useful for physical mapping) Genome databases-(there are over 20 genome databases that can be searched EPD:eukaryotic promoter database NR-non-redundant GenBank+EMBL+DDBJ+PDB. Entries with 100% sequence identity are merged as one. Vector: A subset of GenBank containing vector DNA ProDom PRINTS BLOCKS Types of secondary databases carrying biological infomation

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