Hi Ann, We have several mouse tracks in the genome browser that provide data on the location of microsatellites. I think the first step is for you to read the track descriptions for these tracks and determine which you'd like to use to compare to the DMIT microsatellite data you already retrieved. I have provided the track names and links to their descriptions below.
Microsatellite http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=microsat Simple Repeats http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=simpleRepeat RepeatMasker http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=rmsk It might be helpful to turn on the tracks and view them in the genome browser together to see how they compare. In fact, I have created a session for you in which I have turned on the tracks listed above as well as a custom track of all the DMIT microsatellites from the STS Marker track (this custom track is based on the directions we gave you for finding them originally) and the STS Marker track: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Katrina&hgS_otherUserSessionName=microsatellitesMm9 Once you have decided which track best fits your needs, you can write back to us via the mailing list ([email protected]) and we can assist you in retrieving the data via the Table Browser. Katrina Learned UCSC Genome Bioinformatics Group On 9/16/11 10:19 AM, Ann Eileen Miller Baker wrote: > 16Sp11 > Dear Genome team, > 1. I expand my mouse DMIT microsatellite loci manuscript to include ALL > MICROSATS (tandem repeats from 1 to 6 bp) that are different than > those in Dietrich et al. 1996 NATURE database; i.e., my objective is > determining if my results for Dietrich DMIT are a representative sample of > all mouse microsats. > 2. Can the UCSC team help me find these unknown microsats? If so, > please list steps that I can easily follow (the more detailed the steps the > fewer > emails I will need to send the UCSC team); recall I used the TABLE BROWSER > to find > genomic elements occurring with DMIT loci earlier > Many thanks, > Ann > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
