NCBI BLAST 2.2.15 Release Notes

Major changes include:

    * BLAST now uses a 28-letter protein alphabet supporting the J
(leucine or isoleucine) and O (pyrrolysine) residues.
    * formatrpsdb will now generate RPS blast databases that assume a
28-letter alphabet. These databases are incompatible with rpsblast
versions older than 2.2.15.
    * blastpgp can now combine the e-value from the alignment with a
p-value determined by the composition to yield a unified e-value that is
ultimately used to evaluate the significance of alignments. This
behavior can be enabled with the -t 1u or -t 2u options.
    * megablast now supports incremental ASN.1 output. This behavior can
be enabled with the -D 4 and -D 5 options.
    * BLAST binaries are now available for Windows XP/2003 x64 edition.
    * blastx searches are now significantly faster for queries exceeding
10kbp in length.
    * seedtop can now perform pattern searches even if the pattern is
considered too likely to occur. This behavior can be enabled with the -f
option.
    * BLAST now natively supports the BLOSUM50 and BLOSUM90 score
matrices.
    * BLAST now correctly handles databases restricted by gi lists even
if no sequences will be searched.
    * blastall now prints a header for each query even if queries have
been concatenated.