Question: Changing fasta headers in multifasta file
gravatar for James
5 weeks ago by
APHA Weybridge, UK
James0 wrote:

Hi, Please can anyone help me with this. I have a multifasta file that I want to make a blast database but the header of each sequence is not quite in the correct format. The multifasta has several 100000 sequences in it so really dont want to start again.

correct format should be

>unique-id|my sequence name|etc|etc

I currently have

>notunique___|unique-id|my sequence name|etc|etc

Im pretty sure this should be doable with the sed command but no clue how to do this myself. I want too either just delete 'notunique___|' or replace '>notunique___|' with a new >

notunique is a mix of letters and numbers that are not always the same length of characters.

Any help would be much appreciated

Thank you James

sed • 123 views
ADD COMMENTlink modified 5 weeks ago by genomax44k • written 5 weeks ago by James0

Renaming Entries In A Fasta File

ADD REPLYlink written 5 weeks ago by Sej Modha2.7k

Dear James, you may also be interested in SEDA (, a desktop software that incorporates a lot of functions for processing FASTA files. One of that functions is the "Rename header", which allows you changing headers in different ways. Regards.

ADD REPLYlink written 5 weeks ago by hlfzeus90
gravatar for lieven.sterck
5 weeks ago by
Belgium, Ghent, VIB
lieven.sterck940 wrote:

you can use this perl oneliner:

cat <yourFile> | perl -pi -e 's/>.+?\|/>/g'

on the other hand there should be many other solutions already posted on biostars ;-)

ADD COMMENTlink written 5 weeks ago by lieven.sterck940

Thank you so much lieven.sterck, that worked perfectly.

While there seem to be lots of posts about this stuff I couldn't work out how to change other answers to my exact problem. I really have no experience with these things.

Thanks again James

ADD REPLYlink written 5 weeks ago by James0
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