This directory contain blastz alignments of the Feb. 2003 mouse assembly (mm3) vs. the Jan. 2003 rat assembly (rn2). The axtAll subdirectory contains all alignments, axtBest contains only the best alignment for a particular part of the mouse genome, and axtTight contains a highly conserved subset of axtBest. The alignments are in 'axt' format. Each alignment contains three lines and is separated from the next alignment by a space: Line 1 - summarizes the alignment. Line 2 - contains the mouse sequence with inserts. Line 3 - contains the rat sequence with inserts. The summary line contains 9 blank separated fields with the following meanings: 1 - Alignment number. The first alignment in a file is numbered 0, the next 1, and so forth. 2 - Mouse chromosome. 3 - Start in mouse chromosome. The first base is numbered 1. 4 - End in mouse chromosome. The end base is included. 5 - Rat chromosome. 6 - Start in rat. 7 - End in rat. 8 - Rat strand. If this is '-', the rat start/end fields are relative to the reverse-complemented rat chromosome. 9 - Blastz score. The scoring matrix blastz uses is: 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 then 2200 for the second pass, which just restricts the search space to the regions between two alignments found in the first pass. The alignments were done with blastz, which is available from Webb Miller's group at PSU. Each chromosome was divided into 10010000 base chunks with 10000 bases of overlap. The axtAll alignments include this overlap. The .lav format blastz output, which does not include the sequence, was converted to .axt with PSU's lav2axt. The axtBest alignments were processed with axtBest from Jim Kent at UCSC. 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%.
Name Last modified Size Description
Parent Directory - axtAll/ 2003-05-13 10:16 - axtBest/ 2003-05-13 10:43 - axtTight/ 2003-05-13 10:32 -