Hi Assaf, Our engineer had this to say:
".lav files are only for pair-wise alignments, only two genomes. The MAF files have all the genomes in the multiple alignment." We recommend that you use this program: mafsInRegion which can be obtained from the kent source tree. Information about all of the utilities can be found at: http://genomewiki.ucsc.edu/index.php/Kent_source_utilities Information on how to obtain the source: http://genome.ucsc.edu/FAQ/FAQlicense.html#license3. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: asas asasa <[email protected]> Date: Thu, Aug 25, 2011 at 4:02 PM Subject: [Genome] mapping the chromosomal coordinates of one species to other species To: [email protected] 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
