GenBank

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GenBank

• Nucleotide only sequence database
• Archival in nature
• Data shared nightly among three collaborating
  databases
• GenBank at NCBI
• DNA Database of Japan (DDBJ)
• EMBL at EBI

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The International Sequence Database Collaboration
Source NCBI
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NCBI site map A good place to find resources
http//www.ncbi.nlm.nih.gov/Sitemap/index.html
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GeneBank Release 131.0December 15 2003

• 30968418 Sequences
• 36553368485 Bases

• full release every two months
• incremental and cumulative updates daily
• available only through internet

ftp//ftp.ncbi.nih.gov/genbank/
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GenBank Record

• Header
• information that apply to
• the whole record
• Features
• annotations on the record
• Sequence

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GenBank Record
GeneBank Record
Header
modification date
Molecule Type
Locus Name
Sequence Length
Modification Date
Accession Number
Version Number
GenBank Division
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GeneBank Record
FEATURE
Link to Seq
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GenBank Record
Sequence
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Entrez
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Entrez
http//www.ncbi.nlm.nih.gov/gquery/gquery.fcgi
Select GenBank
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Find mRNA sequence for human epidermal growth
factor receptor
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Specify human as an organism
Click Preview/Index
Specify human by selecting Organisms from
All Fields drop-down menu
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Limit your search
Exclude all technology generated records
Select mRNA in the Molecule list
Select Refseq in the database list
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RefSeq

• Database of reference sequences
• Curated
• Non-redundant one record for each gene, or each
  splice variant, from each organism represented
• Each record is intended to present an
  encapsulation of the current understanding of a
  gene or protein, similar to a review article

RefSeq FAQ
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Molecular databases
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Find Gene Name by searching LocusLink
http//www.ncbi.nlm.nih.gov/LocusLink/
Select organism
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LocusLink
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Find mRNA sequence for epidermal growth factor
receptor (EGFR)
Starts with gene name EGFR

• Limit search to
• Gene Name
• exclude all technology generated records
• Select mRNA as Molecule
• Select Refseq as source database

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Entrez Neighbors and Hard Links
Word weight
3-D Structure
3 -D Structure
VAST
Phylogeny
Protein sequences
BLAST
BLAST
Source NCBI
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SRS List of Public SRS Servers
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SRS List of Public SRS Servers
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SRS Tutorial
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http//srs.ebi.ac.uk
Database Information -which are present -when
indexed
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What is SRS?

• Central resource for molecular biology data
• Data retrieval system
• - more than 250 databanks have been indexed. More
  than 35 SRS servers over the WWW
• Data analysis applications server
• - 11 protein applications
• - 6 nucleic acid applications
• Uniform query interface on the web

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History of SRS

• 1990 - Main author Dr. Thure Etzold
• Development started in EMBL, Heidelberg
• 1997
• Moved to EBI in Cambridge. Development work was
  supported by various grants amongst others from
  the EMBnet.
• 1998
• Etzold and his group join LionBiosciences

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Why SRS?

• Information retrieval
• Easy way to retrieve information from sequence
  and sequence-related databases
• Possibility to search for multiple words/other
  criteria
• Linkage between different databases
• E.g. Find all primary structures with known
  three-dimensional structure
• ... and much more

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Philosophy of SRS
Original database file -plain text, html,
xml
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The Library Select Page
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SRS main toolbar tabs

• Top Page displays databases in different
  database groups
• Query displays either the standard or extended
  query form
• Results or the query manager maintains a
  history of all the results obtained during a
  session
• Projects or the project manager maintains a
  history of all queries and views used during a
  session
• Views allows a user to define a user specific
  view for one or more databases
• Databanks contains a list and some facts about
  the databases available in the system

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Search terms in SRS

• SRS indexed fields can be searched using any of
  the following
• Single word search
• Multiple word phrases
• Numbers and dates
• Regular expressions
• Wildcards