Hi, Lynn! From kent/src/jkOwnLib/genoFind.c:
static int gfNearEnough = 300; int nearEnough = (gf->isPep ? gfNearEnough/3 : gfNearEnough); Nucleotide BLAT: >What is the default constraint on the distance between the two perfect 11-mer matches? 300 bases. > Is this still the default initial match criteria used by the web version of BLAT? yes. Protein BLAT: >What is the default constraint on the distance between theses 4-mers, 100 bases. > and is this still the default initial match criteria used by the web version of protein BLAT? yes. For stand-alone blat, the default minMatch for protein is 1. For gfServer, the default minMatch for protein is 3. Happy aligning! -Galt 7/3/2011 11:16 AM, Young, Lynn (NIH/OD/ORS) [E]: > Greetings, > > Thank you for web access to BLAT. > > According to the 2002 BLAT paper, for the initial match criteria, "nucleotide BLAT uses the two perfect 11-mer match criteria by default." What is the default constraint on the distance between the two perfect 11-mer matches? > > Is this still the default initial match criteria used by the web version of > BLAT? > > I have a similar question for protein BLAT access via the web. The 2002 paper says the default initial match criteria uses 3 perfect 4-mers. What is the default constraint on the distance between theses 4-mers, and is this still the default initial match criteria used by the web version of protein BLAT? > > Sincerely, > Lynn > > Lynn Young, PhD | Informationist/Bioinformatics | NIH Library | National > Institutes of Health | Building 10, Room B1L-306D | 10 Center Drive | > Bethesda, Maryland 20892-1150 | T. 301-594-6426 | F. 301-402-0254 | E. > [email protected]<mailto:[email protected]> | > http://nihlibrary.nih.gov<http://nihlibrary.nih.gov/> | > http://nihlibrary.nih.gov/Bioinformatics | http://twitter.com/bioinformatics1 > _____________________________ > Amazing Research. Amazing Help > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
