Clustering sequences based on sequence similarity

[Shishir]

I have 8000 protein sequences that I want to cluster based on similarity (not identity) and select the longest representative sequence from each cluster. I checked several tools like HiFix, SiliX, ClusTR but could not find the optimal solution. I want to do clustering as like CD-Hit does to reduce dataset but based on sequence similarity rather that sequence identity.

[rhinoceros]

Perhaps USEARCH or if you want something much more complicated, OrthoMCL..

[JackieBadger]

So you want to group by functional similarity?
You can do this based on physio-chemical properties of the amino acids. You translate each amino acid into 5 different metrics and then use Discriminant Analysis of Principle Components to cluster based on these properties.Described here:http://www.biomedcentral.com/1471-2148/12/68

I can provide you with file formats/tips if needs be

[Shishir]

Thanks, it seems interesting and I planned to use it later as currently I am not focused on functional similarity!

So you want to group by functional similarity?
You can do this based on physio-chemical properties of the amino acids. You translate each amino acid into 5 different metrics and then use Discriminant Analysis of Principle Components to cluster based on these properties.Described here:http://www.biomedcentral.com/1471-2148/12/68
I can provide you with file formats/tips if needs be

[Shishir]

Thanks for the reply!

Perhaps USEARCH or if you want something much more complicated, OrthoMCL..