Genomic coordinates for amino acid variation ... how ?

niyl_p · 05-24-2012, 03:05 PM

Want to automate the following...

I have a list of mutations mostly in amino acid change notation (i.e. V600E) ... but can also have CDS syntax (c.1636C>G) ... and I want to find the genomic coordinates of these mutations ...

any ideas would be welcomed ...

Thanks ...

Note: I searched the forum and noticed couple of threads that asked for similar, if not the same, question but didn't find a solution ...

BAMseek · 05-24-2012, 06:30 PM

If these are mutations associated with cancer (such as V600E), you might see if they are already annotated in COSMIC

Another resource worth checking out is Mutalyzer.

If you know the rsIDs, then you can look them up in dbSNP.

Maybe that can at least knock out a few of them . . .

Justin

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05-24-2012, 03:05 PM	#1
niyl_p Junior Member Location: California Join Date: May 2012 Posts: 1	Genomic coordinates for amino acid variation ... how ? Want to automate the following... I have a list of mutations mostly in amino acid change notation (i.e. V600E) ... but can also have CDS syntax (c.1636C>G) ... and I want to find the genomic coordinates of these mutations ... any ideas would be welcomed ... Thanks ... Note: I searched the forum and noticed couple of threads that asked for similar, if not the same, question but didn't find a solution ...

05-24-2012, 06:30 PM	#2
BAMseek Senior Member Location: St. Louis, MO, USA Join Date: Apr 2011 Posts: 124	If these are mutations associated with cancer (such as V600E), you might see if they are already annotated in COSMIC Another resource worth checking out is Mutalyzer. If you know the rsIDs, then you can look them up in dbSNP. Maybe that can at least knock out a few of them . . . Justin