EMBnet Norway -- Release notes for NCBI BLAST 2.2.15
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.