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  • Jocelyn SP
    Junior Member
    • May 2014
    • 1
    #1

    finding SNPs on PlasmoDB

    I have a set of aligned sequences for Plasmodium falciparum, and I want to confirm what strain it is. I have used SNVerIndividual to get a list of SNPs. Now I would like to compare them with known SNPs in the MSP1 region. I can do it on PlasmoDB in a clumsy, visual way, by opening the genome browser for part of the region, having a SNP track, hovering on a SNP diamond and clicking through to the SNP entry to find the distribution of alleles, but obviously I would rather not!
    PlasmoDB has a few searches that look right, e.g. 'Identify SNPs based on Genomic Location (Sanger Sequencing)' but I can't get them to work. I either get all the SNPs in the chromosome, or none.
    Any advice?
    Tags: isolate, plasmodb, plasmodium, snp, strain
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