Find A Protein Cluster Function Using Gotermfinder Module

Question

[Sirus]

Hello every body, I have a group of protein clusters that I want to associate with a function using GO, There is a ready to use perl module called GOTermFinder. they have a script file called "batchGOView" that can be used to do the association. the problem is that the protein IDs in my cluster are UniprotKB IDs and it seems that this script doesn't recognize, is there any way to configure it or at least map my protein IDs to an other database IDs so they could be recognized by that script.

Thank you in advance.

[Pierre Lindenbaum]

show the script please

[Sirus]

Hi, the script is too long and it needs other libraries to work, but if you are interested you can download it from this link.

Answer 1

[Simon Cockell]

Have a look at previous answers to questions such as Programatic technique for gene-name/id conversion. There's a lot of useful information to be found on BioStar already about converting gene/protein identifiers.

Also try searching the site for 'BioMart', since you may find this to be a one-stop-shop for your requirements, and it is easy to write Perl scripts to access it programmatically (in fact, the BioMart website will do it for you).

[Sirus]

Thank you, I will check, in fact I want to know how to configure that script because it has a configuration file and the IDs must be witch format so it can process them.

Answer 2

[Fatcat]

you can download assosiation file from GO, ftp.geneontology.org:/pub/go/gene-associations ,you will find it works with UniprotKB, good luck for you!

[Sirus]

thank you, it seems.