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Old 12-18-2014, 01:09 PM   #2
Brian Bushnell
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Location: Walnut Creek, CA

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This is slightly tangential to your question, but I have a neat tool that will locate a region in a 16S if you have the full-length 16S and primer sequences for the region. It's actually designed for cutting out the sub-regions, but you can just look at the sam file to get the coordinates.

msa.sh in=16S.fasta query=ACTGACTG out=1.sam
msa.sh in=16S.fasta query=ACTGACTG out=2.sam

Those sam files will indicate, for each 16s sequence in the input file, the best alignment of the query sequence (which should be your left or right primer sequence for that subregion). Then you can cut out the regions like this:

cutprimers.sh in=16S.fasta out=V4.fasta sam1=1.sam sam2=2.sam

These are in BBTools.

If you want to align sequences to bacteria, I suggest RefSeq Bacteria (just download and concatenate all of the *.fna.gz files). As far as tools go for BLASTing, you can use BLAST, of course. But I'm not entirely sure what you want. Can you clarify the question?
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