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Removing Sequences With More Than 90% Identity In A Protein Fasta File

I want to remove the sequences which have >90% sequence identity keeping the larger sequence. I am wondering if there is any tool for that.

python
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updated by Frédéric Mahé Frédéric Mahé • written by Pappu Pappu

Say A and B has 90% identity and B is longer; B and C has 90% identity and C is longer. Do you want to remove both A and B?

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written by lh3 lh3

Exactly, I want to remove all the subsets of sequences with >90% identity.

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written by Pappu Pappu

I was not clear: in the example about, A and C do not have 90% identity. Because B has been thrown away, you may think A should be kept as it is not within 90% identity to other chosen sequences. Do you still want to remove A? If you want to remove A, that is single-linkage clustering or equivalently to find connected components in a graph. You can find the algorithm on wiki and many other places. It is pretty simple and should be achievable in <50 lines of Perl.

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written by lh3 lh3

2 answers

  • I just used usearch for nucleotide sequences and I think its quite good. It does single linkage clustering to centroids and reports the centroids and the clusters. Its not open source however.
  • CD-Hit does similar things. But I have not used it.
  • I also tried to do the same with vmatch (also not open source), but the clustering was not good
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written by Ido Tamir Ido Tamir

usearch is freely available if you have an academic email address, and I second Ido Tamir's recommendation. I have used the uclust operation for this.

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written by Josh Herr Josh Herr

T-coffee has a command just for that:

t_coffee -other_pg seq_reformat -in sproteases_large.fasta -action +trim _seq_%%90_
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written by Frédéric Mahé Frédéric Mahé

t_coffee's option removes one of a pair, not both.

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written by ddofer • ddofer

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