Database table

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Mass spectrometry tables

 

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 15, 2018

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