This directory contains alignments of the rat assembly (rn2, Jan. 2003) to the mouse assembly (mm3, Feb. 2003). Files included in this directory: - axtAll directory: all alignments - axtBest directory: filtered set of only the best alignments for a particular region in the mouse genome - axtTight directory: a highly conserved subset of the best alignments for any part of the mouse genome These alignments are in "axt" format. For a description, see http://genome.ucsc.edu/goldenPath/help/axt.html. The alignments were produced by the blastz alignment program, which is available from Webb Miller's lab at Penn State University (http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix used was: A C G T A 91 -114 -31 -123 C -114 100 -125 -31 G -31 -125 100 -114 T -123 -31 -114 91 with a gap open penalty of 400 and a gap extension penalty of 30. The minimum score for an alignment to be kept was 3000 for the first pass and 2200 for the second pass, which restricted the search space to the regions between two alignments found in the first pass. Each chromosome was divided into 10,010,000 base chunks with 10000 bases of overlap. The .lav format blastz output, which does not include the sequence, was converted to .axt with lavToAxt. The axtTight alignments were processed with subsetAxt from Jim Kent using the matrix: A C G T A 100 -200 -100 -200 C -200 100 -200 -100 G -100 -200 100 -200 T -200 -100 -200 100 with a gap open penalty of 2000 and a gap extension penalty of 50. The minimum score was 3400. The axtTight subset covers 6% of the mouse genome while axtBest covers 40%. ----------------------------------------------------------------- If you plan to download a large file or multiple files from this directory, we recommend that you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to the directory goldenPath/mm3/alignments/vsRn2. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) All the files in this directory are freely usable for any purpose.