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Old 12-29-2017, 11:34 AM   #1
Loczi94
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Default How to cluster sequences using HMMER?

Hi everyone!

I have a fasta file with transposons sequences and I have to cluster them using HMMER. Does anyone know how I can do it? I browsed HMMER's documentation but it didn't help..

I hope that someone would be able to help me. Thanks in advance.
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Old 12-29-2017, 11:52 AM   #2
GenoMax
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If you just want to cluster the sequences then CD-HIT would be simpler to use.
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Old 12-29-2017, 11:58 AM   #3
Loczi94
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I clustered the sequences with BlastClust, but now I have to do it using HMMER (it's a part of my project).
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Old 12-29-2017, 12:26 PM   #4
GenoMax
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Are you referring to building a profile HMM rather than a cluster then?
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Old 12-30-2017, 11:18 AM   #5
Loczi94
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No, I'm supposed to group the sequences into clusters. I don't think I need HMM profiles. (Maybe in some latter phases of the project.)
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