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Help needed

Everything on bioinformatics, the science of information technology as applied to biological research.

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Help needed

Postby Jasso » Thu Apr 01, 2010 3:55 pm

Hi.

How I can translate my sequence to ORF sequence in the format of pep.fasta. I am a bit confused because I do not find solution anywhere.
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Postby JackBean » Thu Apr 01, 2010 4:33 pm

you mean to get nucleic acid sequence from amino acid sequence? That's not easy and especially it's not unambiguous, because one amino acid can be coded by up to 6 codons. So, you further work depends on what you want to do. For probing in DNA library, you can look for amino acids coded by one (M, W) or only few codons and use degenerated oligos; for some overexpression you cann look for in-your-(expressing)-species-most-used codons and use these for reverse translation.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re: Help needed

Postby mfursov » Mon Apr 19, 2010 7:46 pm

You can also check this podcast episode: http://www.youtube.com/uniprougene#p/a/u/2/ArEtX9IAyt4
It describes how to find ORFs in DNA sequences.
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Postby fcs » Wed Aug 11, 2010 4:05 am

It sounds like you want to translate the longest ORF sequence to a FASTA sequence.

If that is the case, paste your nucleic acid sequence into this online tool and press the submit button:

http://www.bioinformatics.org/sms/orf_find.html

It will find all the ORFs and even translate them for you.
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