Question: How to cluster (nearest neighbour method) amino acid peptide sequences based on sequence identity?
0
gravatar for vsivaranjanipriya
4.2 years ago by
vsivaranjanipriya30 wrote:

Hi,

 

I have a list of amino-acid peptides. For example:

ILM

FILM

FILVM

..

..

 

Now I need to cluster (nearest neighbour method) these peptides based on sequence identity..

Please suggest any tool to do clustering..

 

Thanks in advance..

alignment • 2.9k views
ADD COMMENTlink modified 4.2 years ago by jockbanan370 • written 4.2 years ago by vsivaranjanipriya30

cd-hit, uclust

ADD REPLYlink written 4.2 years ago by Prakki Rama2.2k

Hi,

try OthoMCL  http://www.ncbi.nlm.nih.gov/pubmed/12952885

http://www.orthomcl.org/common/downloads/software/v2.0/

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Juke-342.0k
0
gravatar for jockbanan
4.2 years ago by
jockbanan370
Czech Republic
jockbanan370 wrote:

If it is just the matter of sequence identity, uclust/cd-hit would probably be the best. If you want to take into account biochemical properties of amino acids used, there are some more sophisticated tools out there, namely: MUSI and the Gibbs sampling tool (IMHO better than MUSI) and also Hammock (there is also a Galaxy version of it), which is suitable especially for very large datasets. 

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by jockbanan370
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