Alignment Free Cog Detection Program
1
4
Entering edit mode
11.8 years ago
Monzoor ▴ 310

Is there any composition program available that can classify a given protein sequene to a COG category without the need for alignment?

tool • 2.1k views
ADD COMMENT
0
Entering edit mode

I too am looking out for such a program. Not for COG finding though. Did someone try to cluster protein sequences using compositional features ?

ADD REPLY
0
Entering edit mode

re Leena In short yes. See i.e. the paper http://www.pnas.org/content/105/40/15352.short

ADD REPLY
0
Entering edit mode

What's a COG category? Can you elaborate on the problem?

ADD REPLY
0
Entering edit mode

It's unlikely such a program could exist. Something as simple as amino acid composition would not be able to accurately discriminate millions of proteins into a few thousand categories.

ADD REPLY
0
Entering edit mode

It's an old question, so you are possibly not looking anymore, but why would you need an alignment free algorithm?

ADD REPLY
2
Entering edit mode
10.9 years ago

As sequence data are so readily obtainable and available and as alignment methods are so robust, this is indeed the preferred mechanism for COG category assignment. I know of no work to assign a protein to a COG without using an alignment of sequence data.

That said, it is possible to ignore or not use sequence alignments, but it is just not routine.

ADD COMMENT
0
Entering edit mode

I have the impression that alignment-free algorithms might be for people who don't believe in evolution lol, so they cannot use it because that would (indirectly) contradict their dogma. For all others, I think they could use the algorithm with best performance.

ADD REPLY

Login before adding your answer.

Traffic: 1857 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6