Amino Acid Variant Call To Dna Snp Call

Question

[Ers]

I would like to convert an amino acid variant to a DNA SNP call. Say you have protein A with mutation G100R, indicating a glycine to arginine switch at position 100.

Assuming the codon position is not in question, does anyone know of an available bioinformatics tool/script that will predict the DNA sequence change(s) causing the amino acid mutation. Ideally, the tool/script would 1) take into account human codon bias and 2) generate probabilities for each prediction?

Not a difficult piece of code to generate, but I would prefer not to reinvent the wheel.

Cheers!

Answer 1

[Larry_Parnell]

It would be much more accurate to use the amino acid variant to query a protein and/or SNP database to find the actual SNP. Due to degeneracy in the codons, there is no perfect correspondence when one goes from amino acid to DNA/SNP. If this is as you indicate work with human data, then why not simply query a list of synonymous and non-synonymous SNPs to find what your research requires - the true, unambiguous DNA change?

Answer 2

[Ers]

Working with data from a mutant screen, which only provides the amino acid change. The codon bias and probability suggestion was intended to deal with the degenerate amino acid code (ie probability would be based upon codon bias)...

Thank you for your response Larry_Parnell. Can you please suggest a database that accepts amino acid queries and returns a SNP?

Answer 3

[Pierre Lindenbaum]

See my tool backlocate described here: http://plindenbaum.blogspot.com/2011/03/mapping-mutation-on-protein-to-genome.html

e.g:

echo -e "EIF4G1\tD240Y" | java -jar backlocate.jar

#User.Gene AA1 petide.pos.1 AA2 knownGene.name knownGene.strand knownGene.AA index0.in.rna codon base.in.rna chromosome index0.in.genomic exon
##uc003fnt.2
EIF4G1 D 240 Y uc003fnt.2 + D 717 GAC G chr3 184040214 Exon 7
EIF4G1 D 240 Y uc003fnt.2 + D 718 GAC A chr3 184040215 Exon 7
EIF4G1 D 240 Y uc003fnt.2 + D 719 GAC C chr3 184040216 Exon 7
##uc010hxy.2
EIF4G1 D 240 Y uc010hxy.2 + D 717 GAT G chr3 184038780 Exon 9
EIF4G1 D 240 Y uc010hxy.2 + D 718 GAT A chr3 184039069 Exon 10
EIF4G1 D 240 Y uc010hxy.2 + D 719 GAT T chr3 184039070 Exon 10
##uc003fnw.2
EIF4G1 D 240 Y uc003fnw.2 + D 717 GAT G chr3 184038780 Exon 8
EIF4G1 D 240 Y uc003fnw.2 + D 718 GAT A chr3 184039069 Exon 9
EIF4G1 D 240 Y uc003fnw.2 + D 719 GAT T chr3 184039070 Exon 9
##Warning ref aminod acid for uc003fnp.2 [240] is not the same (I/D)
EIF4G1 D 240 Y uc003fnp.2 + I 717 ATC A chr3 184039089 Exon 10
EIF4G1 D 240 Y uc003fnp.2 + I 718 ATC T chr3 184039090 Exon 10
EIF4G1 D 240 Y uc003fnp.2 + I 719 ATC C chr3 184039091 Exon 10

(...)

[Ers]

Great tool! Thanks Pierre Lindenbaum!