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Convert Amino Acid Change To Chromosomal Snp Coordinate

How can I convert the amino acid change in certain genes (for example: gene PCP4 : A58S) to the chromosomal coordinate?

What I want is some program which will first look PCP4, find the 58th amino acid, and tell me the three nucleotides in the reference genome which encodes A (alanine).

Thanks

coordinates
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by michealsmith michealsmith

Remember that amino acids are encoded with 3 nucleotide combinations, there's redundancy, and likely several chromosomal coordinates involved that could result in A58S or whatever. What data are you working with?

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written by Alex Paciorkowski Alex Paciorkowski

No, it's A58S in gene PCP4; so there should only be one coordinate, right? I'm just given data like PCP4:A58S (gene name : amino acid change); and I would like to convert this to chromosomal coordinate. Any software that can do this for me?

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written by michealsmith michealsmith

A58S is technically in the protein PCP4 (since that's an amino acid substitution). Since each amino acid is the result of a combination of 3 nucleotides (http://www.cbs.dtu.dk/courses/27619/codon.html) and there are multiple ways this can be encoded, no, there won't be only one genomic coordinate possible.

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written by Alex Paciorkowski Alex Paciorkowski

Ok, I see. What I want is some program which will first look PCP4, find the 58th amino acid, and tell me the three nucleotides in the reference genome which encodes A (alanine). thx

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written by michealsmith michealsmith

1 answer

duplicate of

Amino acid change to Genomic location

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written by Pierre Lindenbaum Pierre Lindenbaum

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