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how remove stopcodons from a GFF

Hi Thank you so much for reading this post. First of all, I would like to say that I am very new to this area of bioinformatics.

I would like to know what tool (preferably using Anaconda) I could use to remove > premature stopcodons, from a GFF file, and how I could use it properly. i executed scipio, but it showed me the next messege:

Warning: Query sequences contain gaps and/or premature stopcodons. It will be necessary to remove them if blat is run separately

And my gff file doesn´t have gaps

Thank you very much

gene genome software error
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updated by Philipp Bayer Philipp Bayer • written by zion22 zion22

hi there, welcome to Biostars. Unfortunately, your question seems a bit incomplete. The comment (that ideally should be code formatting see 101010 button) indicates you use blat. What do you want to achieve? what is your command that fails? GFF is a wide field and I'm unsure whether this is the actual problem.

• 1 views • link
written by Carambakaracho Carambakaracho

1 answer

How are you running scipio?

Looking at the manual, you run scipio with your amino acid fasta file, not your gff file:

scipio.1.4.pl --blat_output=prot.vs.genome.psl genome.fa proteins.aa > scipio.yaml   # takes ~7m

In that case, your input amino acid file has stop codons, which are normally encoded as a '*'. To replace those you can use sed:

sed -i.bak 's/*//g' your_proteins.fasta

This will make a new file your_proteins.fasta.bak as a backup, and the file your_proteins.fasta won't have the stop codons any more.

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written by Philipp Bayer Philipp Bayer

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