Hi Steve, IAP sequences are included in the LTR class of repeats in the RepeatMasker track. To get a custom track consisting only of the positions of the IAP sequences you can create a custom track using the Table Browser. Hit the "Tables" link in the blue bar at the top of the page, and select the following:
group: Variation and Repeats track: RepeatMasker table: rmsk region: genome Now hit "filter: create" and create a filter so that repName does match *IAP* (the stars are wild cards), and hit submit. On themain page, change "output format" to "custom track," name the table whatever you would like, and then hit "get custom track in genome browser." You should now have a track that shows the locations of repeats with names that include "IAP." Note that it is a simplified version of the RepeatMasker track; you will probably want to keep the RepeatMasker track turned on, too, so that you can click through to the details pages and get more information for each element. I hope this is helpful. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/8/11 8:31 AM, Brown, Stephen A wrote: > To all: I am interested in a track that would show me the location > of all IAP sequences in the mouse genome – much like what is > currently available for SINE or LINE elements. Is there such a > thing? Would it be difficult to create one? > > Thanks in advance. > > Steve > > Stephen Brown MD University of Vermont Dept. of Ob/Gyn and > Reproductive Sciences > > _______________________________________________ Genome maillist - > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
