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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.
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Last edited by rhinoceros; 07-09-2013, 02:58 AM.savetherhino.org -
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 beLast edited by JackieBadger; 07-09-2013, 03:55 AM.Comment
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Thanks, it seems interesting and I planned to use it later as currently I am not focused on functional similarity!
Originally posted by JackieBadger View PostComment
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