quickly extract amino acid sequence

mrfox · 02-13-2017, 09:16 AM

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

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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02-13-2017, 09:16 AM	#1
mrfox Senior Member Location: USA Join Date: Aug 2010 Posts: 103	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!

02-13-2017, 09:59 AM	#2
wdecoster Member Location: Antwerp, Belgium Join Date: Oct 2015 Posts: 97	I would assume a quick way would be if you couple bedtools getfasta with a tool such as VEP or snpeff...

02-14-2017, 05:16 AM	#3
SylvainL Senior Member Location: Geneva Join Date: Feb 2012 Posts: 179	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 ...

02-14-2017, 01:37 PM	#5
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	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.