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
