This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Creating Uniqueness In The Set Of Sequences

Hello,

I would like to know how we can filter out the sequences that are more than XX% similar in a set of sequences? I have downloaded sequences from PFAM but there are groups of sequences that are highly similar if not conserved and I want to remove those sequences before making an alignment. Are there any such options in alignment editing programs (Bioedit, Seaview, Jalview,..)?

Thanks

filter sequence similarity
• 2,969 views • link
updated by Martin A Hansen Martin A Hansen • written by Pals Pals

2 answers

CD-Hit is a commonly used program to filter on sequence identity.

• 0 views • link
written by Chris • Chris

Thanks Chris...

• 0 views • link
written by Pals Pals

Usearch/Uclust is well suited for this (better/faster than CD-Hit, but closed source :o/).

• 0 views • link
written by Martin A Hansen Martin A Hansen

Log in to answer this question.

More posts like this