As frustrating as it is to evaluate absolute positions from relative positions, I think Pierre is correct.
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Formatdb And Non Coding Characters
Dear BioStar
I want to use a non coding character, eg X to process snp data. The X helps me to find the snp position in blast hits. However, when I format the blast database from a fasta file containing this character, it gets replaced by N. Is there a workaround for this, so that the X gets reported in the blast result?
thanks for your suggestions.
Jack
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2 answers
I don't think you can do this for a DNA sequence.
The only way is to parse your blast output and to re-map your SNPs.
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You can try using the newest version of Blast and makeblastdb instead of formatdb. There's an option to use an input file with regions to be masked, -mask_data. I cannot guarantee that it will mask with Ns instead of Xs, but it's worth a shot.
EDIT: Check the blast manual here in order to find out how to create a masked database. Another idea for you would be to mask your SNPs with small caps and then search for these patterns in the blast output.
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