Hello: I have been looking for a tool that can compare two lists of multi- block genomic features (or genome alignments in PSL, e.g.) and output the list of features that overlap. I have found the intersectBed (BED format) and the fjoin (GFF format) programs, which do this but in a one block basis, i.e. they intersect one block or exon at a time, regardless of wether other blocks also match or not.
I am interested in annotating microarray probes with genes and transcripts. If a probe align to the genome say, in two blocks separated by a gap, this probe should be annotated to a transcript only if both blocks match (overlap) two consecutive exons in a transcript. I would like to know if you have any program that can do this before I decide if I should write my own. Thank you in advance, Ricardo Verdugo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ricardo A. Verdugo S., D.V.M. Ph.D. Postdoctoral Fellow Gary Churchill Group The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609 [email protected] +1-207-288-6715 +1-207-288-6847 Fax ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
