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quickly extract amino acid sequence

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  • swbarnes2
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    Get flanking DNA sequence for your locus, and do blastx against a database of proteins. Then parse the blastx results. Let blastx figure out the right frame and orientation.

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  • mrfox
    replied
    Originally posted by SylvainL View Post
    It will depend on the frame and orientation... You could make a short script extracting the nucleotides or the region (let's say 5 upstream and 5 downstream) and translate it yourself ...
    Thank you both. Yes it depends on the ORF and orientation. Technically, we have to concatenate the exon DNA sequences of a transcript and count the position of the mutation and translate the short sequences according to the ORF.

    Thanks!

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  • SylvainL
    replied
    It will depend on the frame and orientation... You could make a short script extracting the nucleotides or the region (let's say 5 upstream and 5 downstream) and translate it yourself ...

    Leave a comment:


  • wdecoster
    replied
    I would assume a quick way would be if you couple bedtools getfasta with a tool such as VEP or snpeff...

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  • mrfox
    started a topic quickly extract amino acid sequence

    quickly extract amino acid sequence

    Hi all,

    I wonder if there is a handy tool or database to extract the amino acid sequence of a given coordinate on the human DNA. For example, given chr2:25457242, how to know what is the amino acid it is on and what are the flanking amino acids?

    Thank you!
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