[Genome] question about Blastz parameters

[Michael Beer]

Hi--

I'm trying to reproduce some conservation track results on the UCSC genome browser with multiz.  Could you tell me what parameters were used for Blastz for the Vertebrate Multiz Alignment & Conservation track for genomes: danRer3, tetNig1, fr1, hg18, and mm7?  I am using blastz.v7 and I'm not getting the same blocks as shown in the individual pairwise comparisons shown on this page:

http://genome.ucsc.edu/cgi-bin/hgc?hgsid=90976100&o=25100999&t=25111300&g=multiz5way&i=multiz5way&c=chr9&l=25100999&r=25111300&db=danRer3&pix=1000

Thanks for your help!

Mike Beer




Mike Beer
McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering
Johns Hopkins University
Broadway Research Building 573
733 N. Broadway
Baltimore, MD 21205
mbeer at jhu.edu