Hi Kyle, generateAlignment is not a program -- it is a C function defined in our source code, in the file kent/src/hg/hgc/hgc.c. In that section of the email, I was describing the C code that writes out the alignment that you see on the details page (genome.ucsc.edu/cgi-bin/hgc). If you are an experienced C programmer, you might be able to lift some code from hgc.c to a new program that compiles against our libraries, but there would still be a significant learning curve to understand the data structures that you would need to examine in order to search for mismatches.
Angie ----- "Kyle Tretina" <[email protected]> wrote: > From: "Kyle Tretina" <[email protected]> > To: "Angie Hinrichs" <[email protected]>, "UCSC" <[email protected]> > Sent: Wednesday, March 17, 2010 6:43:28 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Stand Alone Blat Question > > Hello Angie, > > In one of your previous emails, you described the automated way to "Get DNA." > In this description, step six stated: > > 6. Next, the sequences are passed to generateAlignment. Search > backwards in the source to see the definition of generateAlignment. > Note that it calls axtScoreSchemeSimpleDna to get a scoring matrix and > gap penalties, and then passes the sequences and scoring scheme to > axtAffine. See kent/src/lib/axt.c and kent/src/lib/axtAffine.c . The > realignment is printed out block by block using printOffsetAndBoldAxt. > > I would like to know how the program generateAlignment is called/used. Can it > be called in a command line, or perhaps with Blat? Where can I find > information on using this program? > > > > Kyle Tretina > Wheaton College > Junior > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
