Finding a gene of interest in a scaffold

mvaliadi · 12-27-2013, 01:02 PM

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 · 12-27-2013, 03:25 PM

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

http://mummer.sourceforge.net/

mvaliadi · 12-28-2013, 02:28 AM

Many thanks! I'll give that a go!

maubp · 12-28-2013, 06:47 PM

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

GenoMax · 12-29-2013, 05:20 PM

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

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12-27-2013, 01:02 PM	#1
mvaliadi Junior Member Location: Germany Join Date: Dec 2013 Posts: 2	Finding a gene of interest in a scaffold 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?

12-27-2013, 03:25 PM	#2
boetsie Senior Member Location: NL, Leiden Join Date: Feb 2010 Posts: 245	You can align your five genes to the scaffolds with Nucmer (part of MUMmer); http://mummer.sourceforge.net/

12-28-2013, 02:28 AM	#3
mvaliadi Junior Member Location: Germany Join Date: Dec 2013 Posts: 2	Many thanks! I'll give that a go!

12-28-2013, 06:47 PM	#4
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Or make a BLAST database of your assembly, and search the five genes against that?

12-29-2013, 05:20 PM	#5
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	BLAT should be the easiest and quickest solution in a simple case like this. http://genome.ucsc.edu/FAQ/FAQblat.html#blat3