Guy, Sean,... The web site is //psb.stanford.edu/psb-online/proceedings/psb02/ Apparently the pdfs are available. I got one. Pat Burke
On Wed, 28 Oct 2009, Guy Plunkett III wrote: > Sean, > > I found the following description in Dewey CN, Huggins PM, Woods K, Sturmfels > B, Pachter L (2006) Parametric Alignment of Drosophila Genomes. PLoS Comput > Biol 2(6): e73 > <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020073> > > "Assessment of the BLASTZ alignment. A key problem in sequence alignment is > to determine appropriate parameters for a scoring scheme. The standard > approach is to select a model and then to identify parameter values that are > effective in producing alignments that correctly align certain features. For > example, the BLASTZ scoring matrix [17] was optimized for human-mouse > alignment by finding parameters that were effective in aligning genes in the > HOXD region. The BLASTZ scoring scheme is given by a scoring matrix called > HOXD70 [17]." > > Reference 17 is: > Chiaromonte F, Yap V, Miller W (2002) Scoring pairwise genomic sequence > alignments. Proceedings of the Pacific Symposium on Biocomputing. pp. 115-126. > > I don't have access to that journal, but maybe someone else can follow up ... > > Cheers, > Guy Plunkett III > UW-Madison & DNASTAR, Inc. > > On 10/28/09, Sean Conlan wrote: >> Mauve users, >> >> I have used Mauve to align a set of syntenic regions in a group of 7 >> mammals for a colleague's manuscript. One of the reviewers requested >> additional information about the use of the HOXD scoring model. Is >> this documented anywhere (I can't find it in the manual)? From what I >> can tell, it is used for assigning penalties for mismatches, gaps, >> etc... Is there any additional information on how the scoring matrix >> was calculated and its appropriateness for various tpyes of analysis? >> >> Sincerely, >> >> Sean Conlan >> NIH/NHGRI >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and stay >> ahead of the curve. Join us from November 9 - 12, 2009. Register now! >> http://p.sf.net/sfu/devconference >> _______________________________________________ >> Mauve-users mailing list >> Mauve-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/mauve-users > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users > ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
