Sequence Clustering Based On Similarity

Question

[SK]

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.

[KCC]

Are you asking what is the best way to cluster protein sequences or are you just looking for any tool that does what you want? I would assume you could use any tool that clustered on similarity, and then write a script that selects the longest member of each cluster, no?

[Damian Kao]

You mean you want to cluster base on amino acid properties rather than identical protein sequence? What are you referring to when you say 'similarity'?

[Eric Normandeau]

If you know a programming language, you could implement this rather easily. You could blast your sequences against themselves and create your clusters based on similarity (e-value or % identity). Then, it's only a matter of choosing the longest.

Answer 1

[Pablo Marin-Garcia]

this question was cross-posted and answered at http://seqanswers.com/forums/showthread.php?t=31750

Perhaps USEARCH[1] or if you want something much more complicated, OrthoMCL.[1].

[1] http://www.drive5.com/usearch/ [2] http://orthomcl.org/common/downloads/software/v2.0/