nodalpoint.org - Redundancy reduction of sequence sets - Comments

You're welcome

Neil — Thu, 04 Oct 2007 03:44:26 -0400

You're welcome and apologies for omitting "-c 0.9" in my first comment. I'm sure you worked it out.

Thanks !

pansapiens — Wed, 03 Oct 2007 22:37:17 -0400

Thank you Pawel and Neil.

CD-HIT is exactly what I want, and it works great. The algorithm appears to take some smart short-cuts and reduces calculation time from would have taken many hours with my half written brute-force all-against-all pairwise alignment script down to seconds. If CD-HIT is good enough for UniProt, it's good enough for me :)

Blastclust looks like another good option (it was even already installed on my machine ... right under my nose), but is orders of magnitude slower, so I'm sticking with CD-HIT for my quick-n-dirty tasks.

Lucky I didn't go very far coding something to do this myself (although thinking about the problem was enlightening). I've got to remember to listen to my internal "stop-immediately-you-are-reinventing-the-wheel" alarm more often.

I second cd-hit

Neil — Wed, 03 Oct 2007 07:10:33 -0400

CD-HIT works for me. Simple as "cd-hit -i file -o file90 -c 0.9 -n 5".

Sorry about your comments Pawel, they went to spam for some reason.

cd-hit, blastclust

pawel — Wed, 03 Oct 2007 06:43:08 -0400

I'm not sure if my previous comment was saved... Anyway, I will point again to cd-hit and blastclust. However, the first does not make any alignments, and allows some redundancy in the set anyway.

Redundancy reduction of sequence sets

pansapiens — Tue, 02 Oct 2007 20:37:50 -0400

Does anyone have a good (free, open source) software solution to reduce the redundancy of a set of sequences (eg return a set where no two sequences are more than 90 % identical, based on a pairwise alignment) ?