Hello Bryan, One of our engineers had this to say about your inquiry:
Uniqueness, mapability and alignment are similar, but not identical. The number of mismatches tolerated varies between the three measures, as does the window size, and in how surrounding bases affect the measure. See the description pages for each to see how they are calculated. Neither the uniqueness track, nor the mappability track are particularly useful for determining gene homology. They're designed to identify short sequence mappings that are likely to be unreliable. The self-chain can be useful to determine homology, but if something doesn't appear in the self-chain it may still be homologous due to being a an older/younger, or longer/shorter duplication than for which the chain parameters are tuned. Determining homology requires that the researcher determine for themselves exactly what would count as being homologous. The gold standard for determining protein homology is still BLAST. To see the description for any track you can click on the gray bar to the left of the track in the main display or click on the track title above its configuration pulldown menu. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/4/11 2:09 PM, Harrison, Bryan wrote: > Hi, > > I'm having some trouble understanding how and why the Uniqueness and Alignment > used with the mapability feature can be discrepant if they seem to be > measuring > basically the same thing. And when they are discrepant, what might this > suggest > for that region? Additionally, I used the Self Chain function which was > helpful, > but again, did not seem to match with the mapability feature. Is there any way > to use all three of these tools to determine with some certainty if a gene is > or > isn't homologous to another region in the genome? > > Thank you, > Bryan > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
