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Sequence Databases. April 28, 2005

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sequence databases
Sequence Databases
  • April 28, 2005
  • 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.
  • Writing topic
  • Homework#4 and Workshop#4 due today
  • Homework#9 due May 3.
biosequences bioseq
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
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
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
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
Feature Keys
  • Purpose:
    • 1) Indicates biological nature of sequence
    • 2) Supplies information about changes to sequences
  • Feature KeyDescription

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 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
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
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 sequence

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

record from genbank cont 1
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)

record from genbank cont 2
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

record from genbank cont 3
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

record from genbank cont 4
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
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

slide16

Protein databases derived

from GenBank containing

data for a single gene

  • Non-redundant (nr)
  • Swissprot
  • PIR

protein

DNA

RNA

cDNA

DNA databases derived from GenBank

containing data for a single gene

  • Non-redundant (nr)
  • dbGSS
  • dbHTGS
  • dbSTS

RNA (cDNA) databases derived

from GenBank

containing data for a single gene

  • dbEST
  • UniGene
primary databases vs secondary databases
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 primary databases carrying biological infomation
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

Types of secondary databases carrying biological infomation