Hi Or, One of our engineers had this advice:
Please note the discussion of the Default scoring matrix in the "Scoring" section on the page: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html#options_scoring referring to the paper: Chiaromonte F, Yap VB, Miller W (2002). Scoring pairwise genomic sequence alignments. Pacific Symposium on Biocomputing, vol. 7, pp. 115-126. We obtained the non-default scoring matrices from the lastz authors since they had experience in constructing these scoring matrices. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 10/25/11 1:55 PM, Or Zuk wrote: > Dear ucsc team, > > We were looking on statistics of the human 46-way alignments from here: > > http://genomewiki.ucsc.edu/index.php/Hg19_conservation_lastz_parameters > > We are interested in the rate matrix estimated and had a couple of > questions: > > What is the difference between the three matrices presented? > (we see a notable difference between the human-chimp matrix and the other > two). > How were they estimated? > In what units are they presented? > > Best regards, > Or Zuk > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
