Hi all, I would like to build a script that gets start/end chromosomal coordinates of specific species, and rapidly finds the homologous coordinates and strands from other species, or to use such function/program if already exists (maybe in the Jim Kent's source code ?). But, it is important for me to get the coordinates in the maximum bp resolution (as the alignment include gaps, I would like to know where they are located).
Basically, the Multiz alignments in the MAF format, store such information, but I'm wondering if there is an efficient way to extract this information from the files, or from similar files. In addition, the Multiz files are huge, and I'm looking for a more compact storage if exists (e.g., http://www.bx.psu.edu/miller_lab/dist/lav_format.html ). Best wishes, and thanks in advanced for any relevant help, Assaf _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
