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How can I remove ">" sign from whole genome sequence

I have word file of whole genome sequence around 1709 pages, each gene is separated by ">". I need to blast whole genome sequence against a protein sequence from other organism for homology. Is there anyway to remove this information line ">gm_orf648 67_127_d_D 579383 580123 + 741_nt 246_aa" at once. instead of manually deleting one by one.

sequence
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written by Ahmad_Bio • Ahmad_Bio

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written by Pierre Lindenbaum Pierre Lindenbaum

Do not do not do not do not do not keep your sequences in Office formats. Ever.

I’m actually amazed it’s even opened that many pages without crashing.

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written by Joe Joe

Thank you for meaningful help, I managed to copy it in oligo 7 thereby no need to remove > lines.

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written by Ahmad_Bio • Ahmad_Bio

1 answer

The correct answer to your problem is create a blast database from your file and blast the protein against this database - and blast can correctly parse the lines with >.

Your file is in fasta format (also see Is There A Precise Specification For Fasta Files? ). The line you want to remove is part of the format specification:

The first line in a FASTA file started either with a ">" (greater-than) symbol

A fasta file is just a text file, I guess Word is configured to open text files on your computer - but I doubt it is really a Word document.

Virtually all bioinformatics software can correctly parse fasta format, and there is no need to remove these lines.

For the sake of completeness (even if I shouldn't), here is the answer to your original question:

sed -i.bak '/^>/d' file
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written by h.mon h.mon

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