Formatdb And Non Coding Characters

Question

[Yahan]

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

Answer 1

[Pierre Lindenbaum]

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.

[Daniel Standage]

As frustrating as it is to evaluate absolute positions from relative positions, I think Pierre is correct.

Answer 2

[Paulo Nuin]

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.