Finding a gene of interest in a scaffold

[mvaliadi]

Dear all,

I'm having my first go with working with a newly sequenced genome. I have a bacterial genome sequence in scaffolds assembled from 454 data. I want to quickly find out whether this organism contains some genes of interest (5 in total) without going through the whole annotation process for the entire genome.
I have reference sequences from my 5 interesting genes from closely related organisms. My first thought was to do an alignment but the scaffolds are too long and cutting them in fragments might cut through the sequence of interest.

Any alternatives? Is there an easy way to do this?

[boetsie]

You can align your five genes to the scaffolds with Nucmer (part of MUMmer);

http://mummer.sourceforge.net/

[mvaliadi]

Many thanks! I'll give that a go!

[maubp]

Or make a BLAST database of your assembly, and search the five genes against that?

[GenoMax]

BLAT should be the easiest and quickest solution in a simple case like this. http://genome.ucsc.edu/FAQ/FAQblat.html#blat3