quickly extract amino acid sequence

[mrfox]

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]

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

[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 ...

[mrfox]

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]

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.