Database table


	Some useful protein databases for GPMAW:

Name	URL	File*	Procedures*	Comment
Swiss-Prot	ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/	sprot.dat.gz	Convert to DOS Create FastA database Index	Best annotated protein database
Translated EMBL TrEMBL	ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/	trembl.dat.gz	Convert to DOS Create FastA database Index	Autotranslated nucleotide database Supplement to Swiss-Prot
NCBI non-redundant	ftp://ftp.ncbi.nlm.nih.gov/blast/db/	nr.tar.gz	Convert (reduce name line) Index	Not non-redundant, but is non-repeted. Corresponds to the nr database used on NCBI BLAST homepage
IPI human**	http://www.ebi.ac.uk/IPI/IPIhelp.html	ipi.HUMAN.dat.gz	Convert to DOS Create FastA database Index	IPI - International Protein Index Select the “Download the IPI datasets here.” then select file. Minimally redundant but maximally complete combined database
IPI mouse**	http://www.ebi.ac.uk/IPI/IPIhelp.html	ipi.MOUSE.dat.gz	Convert to DOS Create FastA database Index	Select the “Download the IPI datasets here.” then select file. Minimally redundant but maximally complete combined database
IPI rat**	http://www.ebi.ac.uk/IPI/IPIhelp.html	ipi.RAT.dat.gz	Convert to DOS Create FastA database Index	Select the “Download the IPI datasets here.” then select file. Minimally redundant but maximally complete combined database
UniProt	http://www.ebi.ac.uk/uniprot/database/download.html	UniRef100 UniRef90 UniRef50	Convert Index	Clustered sets of protein sequences that show 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) sequence identity
Microbial genome sequences	http://www.ncbi.nlm.nih.gov/genomes/MICROBES/Complet e.html	*.faa FastA files have the .faa extension	Convert Index	A large number of sequenced genomes are listed on this page. Click on the right-hand [F] on the line of the requested genome In the FTP file list, select the .faa file for a FastA formatted file that should be ‘converted’ to DOS before indexing.

* Databases are usually compressed and have to be decompressed before further operations can be done: usually GZipped (.gz or .tar.gz). Programs like gzip, WinZip, StuffIt Expander handles most or all of the file conversion formats.
** For the IPI databases you should download the ‘dat’ files and convert them to FastA using the DBindex utility as in this way cross-indices will be generated that enables GPMAW to retrieve the original database entries (valid from v. 6.10b1). This information will be lost if you download the ‘fasta’ files and use them directly.


	Site last updated: April 14, 2024

Some useful protein databases for GPMAW:

Name

URL

File*

Procedures*

Comment