Running PSIPRED with BLAST+
===========================

NCBI are now encouraging users to switch over from the classic BLAST
package to the new BLAST+ package. On the one hand this is a cleaner
and nicer version of BLAST, but on the other hand, it omits some
useful features. In particular, BLAST+ no longer offers the facility
to extract more precise PSSM scores from checkpoint files in a
"supported" way (previously we used the makemat utility to get this
information).

Unfortunate, BLAST+ saves PSSM data after scaling by 10 and rounding,
which loses too much precision.

One solution would be to patch BLAST+ to offer more precision on the
PSSM file output. This is not a very convenient option - most users
prefer to avoid building BLAST from source. Another solution would be
to generate PSSM data from alignments, but this would entail
generating and reading very large files and would be error prone.

The compromise solution we are trialling is to extract PSSM information
directly from the ASN.1 checkpoint files. This seems to work very well
indeed - though the results are not exactly identical to those from
classic BLAST makemat, as we have to recover the original internal scaling
factor used by BLAST+ with a bit of a hack. The differences appear to
be trivial, however.

Eventually, we will probably switch over to this method as the preferred
way of running PSIPRED, but for the time being the interface to BLAST+
is considered experimental.

If you wish to use PSIPRED with BLAST+, then use the runpsipredplus script
here, rather than the normal runpsipred script. Please do let us know if
you run into insurmountable problems using this script.
