The most commonly adjusted parameters are -F, -e, -b, -v, and -m. The remaining parameters are for more complex searches, which often require optimization that deviates from the default settings. For example, to try to get longer alignment, your can try increasing the X-dropoff values specified by -X, -y, and -Z parameters. To see more hits, we can increase the -e setting and the setting for -v and -b.
As mentioned at the beginning, -e, -b, -v cutoff limits are applied at each of the three alignment steps. The side-effect of stringent settings for those parameters is that certain good HSPs may not be included in the final result. The reason is that their initial HSPs from the un-gapped extension step fall below the cutoff and are not carried to the gapped extension steps.
When BLAST searching with short query sequences, there will not be a reliable way to gauge the statistical significance of the matches due the short nature and biased composition of the query. To make this type of searches work, special parameter/value pairs will be needed. For short nucleotide query, we recommend adding the following parameter/value pairs to the command line:
-F F -e 1000 -W 7
For short peptide queries, we recommend addition the following option/value pairs to the command line:
-F F -e 20000 -W 2 -M PAM30
Please note that blastall does not handle degenerate queries very well. For this reason, we cannot use it to do pattern searches. Instead, we should use seedtop, another program included in the NCBI blast package. For more information, see http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/seedtop.html.