Good Morning Meri: You can read the sequence of events in the alignment procedure in the text file:
http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/doc/sacCer2.txt Look for the section starting: ############################################################################ # DOING MULTIPLE ALIGNMENT WITH OTHER YEAST (DONE - 2009-02-10 - Hiram) It looks like lastz was used without any arguments and the version was: lastz-- Local Alignment Search Tool, blastZ-like (version 1.00.05 built 20080802) I have packaged the pair wise alignments in lav and psl format in the tar gzipped file: http://hgwdev.cse.ucsc.edu/~hiram/sacCer2/sacCer2.pairwise.tgz --Hiram meritxell oliva pavia wrote: > Dear UCSCers, > > I'm interested in comparing the performance of various multiple genome > alignment methods in a yeast 7-way genome alignment. This whole-genome > alignment is precomputed and available in UCSC web > http://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/multiz7way/ > > As far as I know, this alignment was created with the Penn State multiz > alignment tool applied to pairwise alignments which are produced by a > pipeline consisting of the Penn State blastz aligner, followed by the > UCSC chain/net process. I would like to know if blastz pairwise local > alignments used as input for the 7-way alignment are available somewhere > through the UCSC web. Could you provide me the BLASTZ parameters you > used for the alignments, as well as the BLASTZ version? (BLASTZ was > replaced by LASTZ, I don't know up to which point the results for each > method are similar) > > Thanks in advance, > > Meri _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
