-------- Original Message -------- Subject: [blast-announce] BLAST-Announce #056] BLAST 2.2.15 released Date: Fri, 20 Oct 2006 08:37:34 -0400 Notes for the 2.2.15 release BLAST 2.2.15 is now available from the BLAST download page. 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. If you have any questions please write to blast-help at ncbi.nlm.nih.gov Scott D. McGinnis, M.S. DHHS/NIH/NLM/NCBI www.ncbi.nlm.nih.gov -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 or +1 866 888 3112 cell : +1 734 612 4615