Post on 18-Dec-2015
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Sequence Databases
April 28, 2005Learning 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.Writing topicHomework#4 and Workshop#4 due todayHomework#9 due May 3.
BIOSEQUENCES (Bioseq)
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-points out important features at specific locations within the Bioseq
Descriptors-describe entire Bioseq
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.
History of GenBank
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-in other words, 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 a GenBank record.
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
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.
ACCESSION U49845
VERSION U49845.1 GI:1293613
KEYWORDS .
SOURCE baker's yeast.
ORGANISM Saccharomyces cerevisiae
Eukaryota; Fungi; Ascomycota; Hemiascomycetes; Saccharomycetales;
Saccharomycetaceae; Saccharomyces.
Modification dateGenBank division (plant, fungal and algal)
Coding sequenceUnique identifier (never changes)
Nucleotide sequence identifier (changes when there is a changein sequence (accession.version))
GeneInfo identifier (changes whenever there is a change)
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 lineagebased on NCBI Taxonomy Database
Locus name
Record from GenBank (cont.1)
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
Oldest reference first
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)
Record from GenBank (cont.2)
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"
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"
/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
Cutoff
Another location
Another location
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 . . .//
EBI Sequence Retreival System
EMBLSRS-authorSRS-accession numberSRS-titleSRS-referenceSRS-organism
Parts of the record are parsed into separate database files
RNA
cDNA
DNA protein
DNA databases derived from GenBankcontaining data for a single gene
•Non-redundant (nr)•dbGSS•dbHTGS•dbSTS
RNA (cDNA) databases derivedfrom GenBankcontaining data for a single gene•dbEST•UniGene
Protein databases derivedfrom GenBank containingdata for a single gene•Non-redundant (nr)•Swissprot•PIR
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
Types of primary databases carrying biological infomation
GenBank/EMBL/DDBJ
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 secondary databases carrying biological infomation
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