Can you use blastn to check for exact matches?

Question

I need to know on which subjects a query has been matched and where, and this match has to be 100%. Is there a way to do this using blastall?

Thanks.

Answer 1

You can't restrict mapping accuracy to 100% but you can increase the stringency on the E value using the -evalue argument i.e. use a very very small E value. In addition to that, to return back the subject id or accession number as well as the mapping coordinates you can use a custom output format such as this:

-outfmt "6 qacc sacc sseqid evalue qstart qend sstart send"

This will return output in tabular format with 8 columns where: qacc is the query accession, sacc is the subject accession, sseqid is the subject seq-id, evalue is the E value for the alignment, qstart and qend are the query start and end mapping coordinates for the alignment and sstart and send the subject start and end mapping coordinates for the alignment. Putting it all together for an example blastn call:

blastn -query /path/to/myquery.fasta -db /path/to/db -evalue 0.001 -out /path/to/myoutput.tsv -outfmt "6 qacc sacc sseqid evalue qstart qend sstart send"

blastn -help will give you more options on the custom output format.