Information organization Oct 2, 2012 Learning objectives-Demonstrate Dotter Program. 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. Homework #2 due today. Homework #3 due Tues. Oct. 9
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Information organization
Oct 2, 2012Learning objectives-Demonstrate Dotter Program. 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.Homework #2 due today.Homework #3 due Tues. Oct. 9
What is GenBank?
Gene sequence database
Annotated records that represent single contiguous stretches of DNA or RNA-may have more than one coding region.
Generated from direct submissions to the DNA sequence databases from the authors.
Part of the International Nucleotide Sequence Database Collaboration.
Began with Atlas of Protein Sequences and Structures (Dayhoff et al., 1965)In 1986 it shared data with EMBL and in 1987 it shared data with DDBJ.Primary databaseExamples of secondary databases derived from GenBank: UniProt, EST database.GenBank Flat File is a human readable form of a GenBank record.
Transcription
5’
5’
3’
3’Promoter
Coding strand
Template strand
Transcription
initiation site
Transcription
termination site
Protein Coding Sequence (CDS)
5’ untranslated region (5’UTR)
3’ untranslated region (3’UTR)
Downstream (relative to CDS)Upstream (relative to CDS)
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
Feature Keys
Purpose: 1) Indicates biological nature of sequence 2) Supplies information about changes to
sequencesFeature Key Description
conflict Separate determinations of the same seq. differ rep_origin Origin of replication protein_bind Protein binding site on DNA CDS (Protein) coding sequence
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 that has a product called “alcohol dehydrogenase” and corresponds to the gene called “adhI”.
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.
Record from GenBank
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.
Partial sequence on the 5’ end. The 3’ end is complete.
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)
Keys
Location
Qualifiers
Descriptive free text must be in quotations
Start of open reading frame
Database cross-refsProtein sequence ID #
Note: only a partial sequence
Values
Record from GenBank (cont.3) gene 687..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"