Protein to genomic alignment

[keliyo]

Hi all,

I am trying to locate the genes that encode for a specific protein from the genome data that have been generated by whole genome sequencing.

After genome assembly, I have about 4000 contigs. I have about 100 amino acid sequences of a specific protein from different organisms and I am trying to align these sequences to the genome sequences that I have to look for clues of putative homology, domain or motifs.

Anyone here can tell me what are the programs that can do a many to many alignment between protein and genomic sequences? Many to many as in I need to align all 100 amino acid sequences to my 4000 contigs all at the same time.

Please help! Thank you very much. Your suggestions are very much appreciated.

[Gig77]

genBlastG should work fine in such a setting.

[keliyo]

genBlastG should work fine in such a setting.

Hi there Gig77, thank you for your suggestion. But, does genBlastG work for many to many alignment? as in can it accept more than 1 query seq and more than 1 target sequence?

[Wallysb01]

Exonerate is often used for this.

http://www.ebi.ac.uk/~guy/exonerate/

[Gig77]

Hi there Gig77, thank you for your suggestion. But, does genBlastG work for many to many alignment? as in can it accept more than 1 query seq and more than 1 target sequence?

Yes it can.

[keliyo]

Exonerate is often used for this.

http://www.ebi.ac.uk/~guy/exonerate/

Thanks Wallysb01. I will give it a try!

[keliyo]

OK. got it. Thanks Gig77.