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I'm sure this is a basic question, but I couldn't find an answer anywhere. Let's say I'm provided with the location of an amino acid or a nucleotide (for example, which lists the location as the ACADM gene, 985A>G (the nucleotide polymorphism) and 304 as the amino acid mutation (from Lys>Glu)). How would I go about now identifying the exact position of this on the chromosome? Eg: Chromosome 1, location 76123456?

Currently the only way I can think is to manually count 304 amino acids, or 985 nucleobases, from the start of the gene where the start location is listed. However this isn't practical. I downloaded some software (IGV & GenomeViewer) and can't see a way I can view the actual amino acid or nucleobase number from the start of the gene.

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Option 1: You can use the SNP database, to see if it has (and it usually is) characterised before: The tutorial is here (http://www.sciencebuddies.org/science-fair-projects/project_ideas/BioMed_Bioinformatics_NCBIGene_SNP.shtml)

Option 2: is to use a go to character function in a few text editors. If you are on windows, You can do it in Notepad++ (https://superuser.com/questions/487507/how-can-i-find-nth-character-in-notepad); if in Linux/mac, you probably know how to do it in vim (https://stackoverflow.com/questions/22862558/go-to-a-specific-offset-in-a-document). If using other text editors in Linux, ask around that community, and they'll tell you how to go about it.

Option 3: One another labour intensive but easy way to do it is to use the tools available online. I personally use NCBI for this, and play around with the region shown. This prevents you from counting. Once you get the local region, select a few nucleotides to the left and right, and use that as a search term in your sequence (find text and replace text)

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Option 4: And my personal favourite, get the computer to do it for you like this: https://stackoverflow.com/questions/23662748/replace-a-nucleotide-at-a-certain-position-in-a-dna-sequence-file

If you are using IGV, it is said in the documentation here (https://www.broadinstitute.org/igv/Navigate) on how to search for regions and even insert mutations. Were you not able to make this work ?

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  • $\begingroup$ Some really helpful options there, thanks Rover. I'm going off 23andme data, and it seems it has listed the locations different to the ch38 genotype. Unfortunately it seems the SNP's in the NBI are also missing the 304 variant. Would I be correct in saying no SNP exists for the 304? $\endgroup$
    – user4779
    Commented May 2, 2015 at 17:32

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