This directory contains alignments of the rat assembly (rn3, Jun. 2003) to the human assembly (hg16, Jul. 2003). Files included in this directory: - axtNet directory: contains chained and netted alignments, i.e. the best chains in the genome, with gaps in the best chains filled in by next-best chains where possible. - axtTight directory: contains a highly conserved subset of the best alignments for any part of the human genome. The alignments in the axtNet and axtTight directories 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 5000 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 10,100,000 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 axtNet alignments were processed with chainNet, netSyntenic, and netClass written by 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. ----------------------------------------------------------------- If you plan to download a large file or multiple files from this directory, we recommend 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/hg16/vsRn3/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) All the tables in this directory are freely available for public use. -------------------------------------------------------------------- References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte, F., Yap, V.B., and Miller, W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002;115-26. Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20):11484-11489 Sep 30 2003. Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-mouse alignments with BLASTZ. Genome Res. 13(1):103-7 (2003).