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How to remove gap-only columns from a multiple sequence alignment in FASTA with Jalview and how to edit genes? Also, how to extract genes without gaps from an alignment on Linux?

Hello everyone,

I have a multiple sequence alignment in FASTA format, and I am using Jalview to visualize and edit it.

  1. How can I remove columns that contain only gaps from this alignment using Jalview?
  2. How can I edit genes directly in the alignment with Jalview?
  3. Alternatively, is there a way to extract gene sequences without gaps from an alignment using Linux command line tools or scripts?

Here is a small example of my alignment (FASTA format) enter image description here

I want to get rid of gap-only columns (positions where all sequences have '-') and obtain gap-free gene sequences.

Thanks in advance for your help!

Best regards, Ivalda

fasta alignment jalview
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written by ivaldakoyo • ivaldakoyo

1 answer

How can I remove columns that contain only gaps from this alignment using Jalview?

There should be no columns that contain only gaps unless you made an alignment and later removed some sequences from it. What would be the purpose for the alignment programs to randomly insert a gap into all sequences? What's more likely is that you have one or two sequences that have a residue at those positions where all others have gaps, and sometimes it is difficult to spot them.

Alternatively, is there a way to extract gene sequences without gaps from an alignment using Linux command line tools or scripts?

trimAl can remove columns based on the percentage of gaps in it. For example, you can remove all the columns that have more than 50% gap characters in them. There are many other options.

https://vicfero.github.io/trimal/

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written by Mensur Dlakic Mensur Dlakic

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