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 | ||
+ | |||
+ | 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 == | == 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:
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) |