-----Forwarded Message----- Date: 15 Aug 2003 10:56:28 -0400 Now available on the NCBI BLAST web pages is a new type of nucleotide search called Discontiguous MegaBLAST (http://www.ncbi.nlm.nih.gov/blast/discontiguous.html). Like MegaBLAST, this service uses a greedy algorithm and concatenates queries to save time scanning the databases. But instead of using exact matches to database sequences for initial hits, it finds matches to a discontiguous template made from the query. This results in fewer initial words but more statistically significant alignments. This makes Discontiguous MegaBLAST good for comparison of divergent sequences, especially from different organisms, which have alignments with low degree of identity but perhaps encode similar proteins. Discontiguous MegaBLAST can be found on the main NCBI BLAST web page at http://www.ncbi.nlm.nih.gov/BLAST/ It is also included in the WWW BLAST server located at (ftp://ftp.ncbi.nih.gov/blast/server). Discontiguous MegaBLAST searches can also be done using Standalone BLAST. To do this, you can specify in the megablast binary, template length option, with the -t parameter and the Template Type with parameter -N. The word size (-W) must also be set to 11 or 12 for Discontiguous MegaBLAST seaches. For any questions please contact blast-help@ncbi.nlm.nih.gov. -- Joseph Landman, Ph.D Scalable Informatics LLC email: landman@scalableinformatics.com web: http://scalableinformatics.com phone: +1 734 612 4615