Blast+help+desk+email+9-25-12

To: blast-help@ncbi.nlm.nih.gov Subject: blastp command line parameters

Message: Hi BLAST help representative,

I want to adjust my blastp command line search to search for short input sequences. This webpage (under the "The protein version of "Search for short nearly exact matches" is optimized to find matches to a short peptide sequence." section) had some great tips about how to adjust the parameters for this procedure: http://www.ncbi.nlm.nih.gov/blast/Why.shtml

I followed most of these suggestions to give a command like this: ./blastp -db nr.00 -query pqregs.fsa -word_size 2 -evalue 20000 -num_descriptions 20000 -matrix PAM30 -out results.out

I was able to obtain many of the type of results I was expecting. However, I was not able to obtain these types of results when giving a command like this: ./blastp -db nr.00 -query pqregs.fsa -task blastp-short -out results2.out

The "-task blastp-short" command did not seem to help me as I thought it would.

Now I would like to know how I can turn off composition based statistics and the seg filter from the parameters on the command line. When I type blastp help I see that there are parameters for -comp_based_stats compo] and -seg SEG_options]