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Old 02-13-2017, 09:16 AM   #1
mrfox
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Default 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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Old 02-13-2017, 09:59 AM   #2
wdecoster
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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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Old 02-14-2017, 05:16 AM   #3
SylvainL
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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 ...
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Old 02-14-2017, 06:22 AM   #4
mrfox
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Quote:
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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Old 02-14-2017, 01:37 PM   #5
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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