Difference between revisions of "Sources iRefIndex 5.0"

From irefindex
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Last edited:08th, July 2009
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Applies to iRefIndex release: 5.0
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Release date:  July 2009
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Authors: Ian Donaldson,Sabry Razick and Paul Boddie
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Database: iRefIndex (http://irefindex.uio.no)
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Organization: Biotechnology Centre of Oslo, University of Oslo (http://www.biotek.uio.no/)
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Description: This file lists interaction and protein sequence related resources used for the current build of the iRefIndex.
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Statistics for the iRefIndex are available and include a breakdown of interactors and interactions from each data source.
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*For statistics on full public dataset please refer to:
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*For statistics on the public dataset (distributed on the FTP site contains) please refer to:
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== Sequence related resources ==
 
== Sequence related resources ==
  

Revision as of 08:45, 8 July 2009

Last edited:08th, July 2009

Applies to iRefIndex release: 5.0

Release date: July 2009 Authors: Ian Donaldson,Sabry Razick and Paul Boddie

Database: iRefIndex (http://irefindex.uio.no)

Organization: Biotechnology Centre of Oslo, University of Oslo (http://www.biotek.uio.no/)

Description: This file lists interaction and protein sequence related resources used for the current build of the iRefIndex. Statistics for the iRefIndex are available and include a breakdown of interactors and interactions from each data source.

  • For statistics on full public dataset please refer to:
  • For statistics on the public dataset (distributed on the FTP site contains) please refer to:


Sequence related resources

Source Format Location Version (date)
SEGUID Tab-delimited text ftp://bioinformatics.anl.gov/seguid/ seguidannotation September 23rd, 2008
UniProt Text http://beta.uniprot.org/downloads
Download : 1.UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) 2.UniProtKB/TrEMBL (uniprot_trembl.dat.gz)
UniProt Release 15.3 (May 26th 2009)
UniProt, IsoForms FASTA http://beta.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz Release 15.3 (May 26th 2009)
UniProt, SGD Tab-delimited text file. http://www.expasy.org/cgi-bin/lists?yeast.txt Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD Release:57.3 (May 26th 2009)
UniProt, FLY Tab-delimited text file. http://www.expasy.org/cgi-bin/lists?fly.txt Drosophila: entries, gene names and cross-references to FlyBase. Release: 57.3 (May 26th 2009)
NCBI, RefSeq GenPept ftp://ftp.ncbi.nih.gov/refseq/release/complete see *.protein.gpff.gz files Release 35 (May 4th, 2009)
NCBI, MMDB/PDB Tab-delimited text ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table (Downloaded on May 14th, 2009)
NCBI, PDB sequences FASTA ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz (Downloaded on May 14th, 2009)
NCBI Gene2Refseq Tab-delimited text ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz (Downloaded on May 14th, 2009)