Hello Peng, Very sorry, your reply went to the genome mailing list only, not to your email address as well. Our apologies.
Here is the posting: https://lists.soe.ucsc.edu/pipermail/genome/2010-April/022012.html Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/24/10 12:09 PM, Peng Yu wrote: > Could somebody answer me the following question? > > On Wed, Apr 21, 2010 at 2:48 PM, Peng Yu<[email protected]> wrote: >> I'm wondering what "some sort of gap penalty" refers to. Also I query >> 25bp sequence using the default, BLAT still gives the result. By >> definition 25bp sequence should at most have a score of 25, which is >> less than 30. Why the query still returns the the result? >> >> -minScore=N sets minimum score. This is the matches minus the >> mismatches minus some sort of gap penalty. Default is 30 >> >> >> -- >> Regards, >> Peng >> > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
