Hello Dhiral, For more information on the chain generation process please see this wiki:
http://genomewiki.ucsc.edu/index.php/Chains_Nets You can also read the methods section of any of the description pages for the Chain/Net tracks. These can be accessed by clicking on the gray bar to the left of the track in the main display or by clicking on the track title above the pulldown menu: http://genome.ucsc.edu/cgi-bin/hgTrackUi?&c=chr21&g=chainNetOviAri1 There may be no easy way to calculate the maximum number of mismatches that could appear in any particular gapless block as it depends on the blastz/lastz parameters, the minimum chain score used in the chaining, and on how high scoring any flanking alignments are. For the species that appear in the hg18 44-way, the various parameters appear here: http://genomewiki.cse.ucsc.edu/index.php/Hg18_44way_blastz_parameters Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 5/5/11 7:36 AM, Dhiral Phadke wrote: > Hi, > > I was looking at the description of the chain files at: > http://genome.ucsc.edu/goldenPath/help/chain.html and have some questions: > > > 1. What does the chain score represent? How is it computed? > 2. The alignment data lines contain the size of the ungapped alignment. How > many > mismatches are allowed in each ungapped alignment? > > 3. What tool is used to do the alignments? > > Thanks a lot for your help! > > -Dhiral. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
