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

Question

[Ahmad_Bio]

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.

[Pierre Lindenbaum]

Perhaps bioinformaticians should just give up and rewrite tools to accept sequences in Word fasta format :)

— Mick Watson (@BioMickWatson) January 31, 2012

[Joe]

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.

[WouterDeCoster]

You don't have to delete these.

[Ahmad_Bio]

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

Answer 1

[h.mon]

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