How can I pick out prokaryotic sequences from a multiple sequence alignment file?

Question

[Chong Tang]

How can I pick out prokaryotic sequences from a multiple sequence alignment file?

I have a huge MSA file containing over 1,000 sequences which is in a typical clustal format. If I want to select those prokaryotes sequences from this msa file and create a new msa file. What should I do?

[Asaf]

What are the names of the sequences? TXIDs? Organism name? The first step would be to get a list of the desired sequences' names.

Answer 1

[Brett]

A non sophisticated way of doing it, would be to cut and paste all the accession numbers into the PIR database http://pir.georgetown.edu/pirwww/index.shtml

This will bring up all the details for all the sequences.

Select from drop down box filters, and select TAXA ID. In this field simply enter 2 (for Prokaryotes) and the results will be filtered. Then click select all and then there is an alignment button (in Jalview) on top right of results.

Depending on your alignment naming/ID DAVID might be handy for converting the initial sequences into a format PIR can accept.