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-   -   quickly extract amino acid sequence (http://seqanswers.com/forums/showthread.php?t=74208)

mrfox 02-13-2017 09:16 AM

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!

wdecoster 02-13-2017 09:59 AM

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

SylvainL 02-14-2017 05:16 AM

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 ...

mrfox 02-14-2017 06:22 AM

Quote:

Originally Posted by SylvainL (Post 204211)
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!

swbarnes2 02-14-2017 01:37 PM

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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