Difference between revisions of "Sources"

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== Sequence related resources ==
 
== Sequence related resources ==

Revision as of 10:32, 6 November 2008

Last edited: November 11th, 2008 Applies to iRefIndex release: beta 2.0 Release date: November 11th, 2008 Authors: Ian Donaldson and Sabry Razick 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.


Interaction related resources

Source Format Location Version (date)
BIND, Tab-delimited text file. ftp://ftp.bind.ca/pub/BIND/data/bindflatfiles/bindindex/ 20050525.complex2refs.txt 20050525.ints.txt 20050525.refs.txt 20050525.complexes.txt 20050525.labels.txt 20050525.complex2subunits.txt These file are no longer available via ftp but are available from the authors. BIND archival content is now managed by Thomson Scientific. See http://bond.unleashedinformatics.com/ 05/25/05
BioGRID PSI-MI 2.5 http://www.thebiogrid.org/BIOGRID-ORGANISM-2.0.45.psi25.zip Version 2.0.45
DIP PSI-MI 2.5 http://dip.doe-mbi.ucla.edu/dip/Download.cgi dip20080708.mif25 07/08/08
HPRD, PSI-MI 2.5 http://www.hprd.org/download/HPRD_SINGLE_PSIMI_090107.xml.tar.gz Release 7. September 01, 2007
IntAct, PSI-MI 2.5 ftp://ftp.ebi.ac.uk/pub/databases/intact/2008-08-22/psi25/ pmidMIF25.zip August 22, 2008
MINT PSI-MI 2.5 ftp://ftp://mint.bio.uniroma2.it/pub/release/psi/2008-04-07/full.psi25.zip April 07, 2008
MPact PSI-MI 2.5 ftp://ftpmips.gsf.de/yeast/PPI/ mpact-complete.psi25.xml April 19, 2007
MPPI PSI-MI 1.0 http://mips.gsf.de/proj/ppi/data/mppi.gz Not available
OPHID PSI-MI 1.0 http://ophid.utoronto.ca/ophid/downloads.html (This service no longer available, please refer to http://ophid.utoronto.ca/ophidv2.201/) 07/18/06

Sequence related resources

Source Format Location Version (date)
SEGUID Tab-delimited text ftp://bioinformatics.anl.gov/seguid/ seguidannotation 07/24/07
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 13.1 (March 18, 2008)
UniProt, IsoForms FASTA http://beta.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz 03/18/08
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: 55.1 (18-Mar-2008)
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: 55.1 (18-Mar-2008)
NCBI, RefSeq GenPept ftp://ftp.ncbi.nih.gov/refseq/release/complete see *.protein.gpff.gz files Release 28 (March 9, 2008)
NCBI, MMDB/PDB Tab-delimited text ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table 03/20/08
NCBI, PDB sequences FASTA ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz 03/20/08
NCBI Gene2Refseq Tab-delimited text ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz 03/21/08