Hi Mariano, There is an'OligoMatch' tool in the source tree which may be of interest to you (src/hg/utils/oligoMatch). The usage statement is as follows:
oligoMatch - find perfect matches in sequence. usage: oligoMatch oligos sequence output.bed where "oligos" and "sequence" can be .fa, .nib, or .2bit files. Each motif can be used with this command to build a bed file with a number of different motif matches. I hope this helps. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Mariano Loza Coll wrote: > Hello, > > I would like to display different short sequence matches to the same > region of a genome (for instance, mark the presence of putative > binding sites for different transcription factors to the same stretch > of DNA). > > Is there a way to add several Short Match tracks through the browser, > each with its own motif recognition. Alternatively, is there a way to > code several different oligoMatch track lines to custom track and > browser lines? > > Alternatively-2, is there a way to specify different recognition > motifs within the same Short Match track (ie. to display matches to 2 > or more sequence matches)? > > I did browse previous discussion threads on this, and it seems like it > won't be easy, but I figured I'd give it a try... > > Thanks a lot in advance, > > Mariano > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
