Consensus Sequence And Assembly Of Multiple Group Of Sequences

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11.1 years ago

Nicolas Rosewick 11k

Hi,

I've a little question about consensus sequences. So I've a bunch of small overlapping sequences from different groups and I want to regroup sequences from the same group together and compute the consensus sequences. The thing is that I don't know from which group sequences are coming

A little example is better to understand (here there are thre groups - line 1-4 : g1 ; line 5-8 : g2 ; line 9-12 : g3):

AAATTTGGGCCC
AAATTTGGG
AAATTTG
   TTTGGGCCCAAA
ATGCATGCAT
ATGCATGC
  GCATGCATGC
 TGCATGCAT
ACGTACGTACGT
ACGTACGTA
  GTACGTACGTAC

And the expected output would be :

Group1 : AAATTTGGGCCCAAA

Group2 : ATGCATGCATGC

Group3 : ACGTACGTACGTAC

The problem is to cluster the sequences together to form the groups. After the consenus sequence is pretty simple to do.

Anyone has an idea ?

Thanks

N.

consensus • 2.5k views

ADD COMMENT • link updated 6.7 years ago by Biostar 20 • written 11.1 years ago by Nicolas Rosewick 11k

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If you are just looking for Clustering then blastclust would do.

ADD REPLY • link 11.1 years ago by always_learning ★ 1.1k

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or maybe CD-HIT http://weizhong-lab.ucsd.edu/cd-hit/

ADD REPLY • link 11.1 years ago by Biomonika (Noolean) 3.2k

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"After processing" with what?

ADD REPLY • link 11.1 years ago by PoGibas 5.1k

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I edited my question.

ADD REPLY • link 11.1 years ago by Nicolas Rosewick 11k

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Maybe use CAP3?

ADD REPLY • link 11.1 years ago by Damian Kao 16k

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