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Building A Consensus Sequence From A Set Of Sequences

I have a list of around 50 pdb files/fasta sequences (they do not belong to any family). I badly need to build up 10-15 consensus sequences from them representing sets of PDB files. I have used the web servers ClustalW and Consensus could not really understand the results. Please help.

Rishika CARLBio group

multiple clustalw consensus bioperl
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updated by brentp brentp • written by Rishika Sengupta • Rishika Sengupta

4 answers

I have once found the program PAGAN to be useful in this sort of cases. You could go through the Manuscript first. Also Codoncode aligner can address your problem.

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written by Pals Pals

Probably because it is targeted to debian based linux environment. It would be really difficult if not impossible if you are using other linux distributions.

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written by Pals Pals

You need libboost libraries installed: sudo apt-get install libboost-dev libboost-program-options1.42-dev libboost-regex1.42-dev

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written by 2184687-1231-83- 2184687-1231-83-

If you have problems installing PAGAN, please contact the author and ask for help. You can find the contact details on the program web site.

PAGAN requires two Boost packages (available for all platforms, including OSX and Windows) but shouldn't then compile fine.

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written by Ari • Ari

If you have problems installing PAGAN, please contact the author and ask for help. You can find the contact details on the program web site. PAGAN requires two Boost packages (available for all platforms, including OSX and Windows) but should then compile fine.

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written by Ari • Ari

If what you want to do is cluster the sequences into groups and choose a representative of each group, look no further than CD-HIT. It has a web server too, if you don't want to run it locally.

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written by Neilfws Neilfws

I have just now used the CD-HIT web server. But I want to input my sequences in fasta format, cluster the sequences into groups and choose a representative of each group, as you said correctly. Can I do that with the help of CD-HIT? Please reply. Thank you so much for your help.

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written by Rishika Sengupta • Rishika Sengupta

Well yes, you can - as I said in the answer.

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written by Neilfws Neilfws

Well yes, you can - as I said in the answer. I've used the standalone program to do exactly that; I have not used the server, but assume it can do the same.

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written by Neilfws Neilfws

Thanks a tonne....could do that after installing the G++ compiler. :):)

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written by Rishika Sengupta • Rishika Sengupta

After generating your clusters, look here for how to generate a consensus sequence.

Every time someone asks about consensus sequences, I recommend motility. It has a C++ and a python interface.

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updated by Ram Ram • written by brentp brentp

Will this program consider protein sequences also?

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written by Pals Pals

But will this program consider protein sequence also?

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written by Pals Pals

@Kisun, good point. You'd have to convert to nucleotide sequence to use motility.

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written by brentp brentp

How about doing it with R?

the Biostring package is very helpfull and easy to understand. have a look at the vignette of Biostring

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written by Assa Yeroslaviz Assa Yeroslaviz

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