Gene Function through sequence homology

Question

[siddharth.avadhanam]

Hi

So I've got list of genes putatively involved in Leptospira virulence, and I want to produce hypotheses on their function through sequence homology. So I was thinking of BLASTing them as a first step, but I'm not to sure how I would interpret the results. Are there better ways of going about this ? Any sort of resources that would help a beginner out with this task?

Thanks in advance :)

[Manvendra Singh]

do you want to see the conservation of found genes ?

what is your ultimate goal from gene list. do you want to know conserved domain, conserved function, conserved regulation or anything else?

[siddharth.avadhanam]

Conserved function would be my ultimate aim

[Manvendra Singh]

I would suggest you to go for gene ontology first. Create different sub-groups of genes on the basis of their Molecular function, Biological Processes, there are many tools out , see that which fits best.

Then probably look into conservation scores of their sequences in each sub-groups

[siddharth.avadhanam]

Should I work using proteins. I read that this would be a better approach to identifying significant sequence homology. I'm just unsure about the process involved behind inferring a (hypothetical) function. This is my ultimate aim. I'm sure this is a common problem in evolutionary studies, and I don't want to reinvent the wheel, so what are the classical approaches to this problem? Any paper / guides that you can refer me to?

[rwn]

How about Blast2GO? It takes a set of fasta files (nucl or protein), runs BLAST and infers functions based on gene ontology information. It's a bit broad-brush perhaps, but good for an overview of what you have. Easy to use as well.

[siddharth.avadhanam]

Thanks. I'll look into it.

Answer 1

[cdsouthan]

Run them through the InterPro engine unless UniProt has already done it for you

Answer 2

[skjobs]

blast2GO is the tool where the will annotate your genes on the basis of known function. If you want to know on the basis of the functional domain such as domain, motif or fold then i would suggest you to align the sequences with the pfam database of other annotation database.