This directory contains alignments of the following assemblies: - target/reference: Mouse (mm3, Feb. 2003, NCBI Build 30) - query: Rat (rn3, June 2003, Baylor HGSC v. 3.1) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - all.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - mouse.net.gz: "net" file that describes rearrangements between the species and the best Rat match to any part of the Mouse genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html . These alignments were produced after doing a swap of the rn3/mm3 blastz alignments. Initially, the rn3 and mm3 assemblies were aligned by the blastz alignment program, which is available from Webb Miller's lab at Penn State University (http://www.bx.psu.edu/miller_lab/). Any rn3 sequences larger than 10,010,000 bases were split into chunks of 10,010,000 bases overlapping by 10,000 bases for alignment. A similar process was followed for mm3, with chunks of 30,000,000 overlapping by 0. Following alignment, the coordinates of the chunk alignments were corrected by the blastz-normalizeLav script written by Scott Schwartz of Penn State. Transposons that have been inserted since the Mouse/Rat split were removed from the assemblies before alignment using the fasta-subseq and strip_rpts programs from Penn State. The abbreviated genomes were aligned with blastz, and the transposons were then added back in (i.e. the alignment coordinates were adjusted) using the restore_rpts program from Penn State. The blastz scoring matrix (Q parameter) used was the mus_rat.q matrix: A C G T 75 -131 -53 -156 -131 100 -133 -53 -53 -133 100 -131 -156 -53 -131 75 with a gap open penalty of O=400 and a gap extension penalty of E=30. The minimum score for an alignment to be kept was K=3000 for the first pass and L=50000 for the second pass, which restricted the search space to the regions between two alignments found in the first pass. The minimum score for alignments to be interpolated between was H=2000. The X-drop parameter for gapped extension was set to Y=3400. T=2 (12of19 without transitions) was also used. The .lav format blastz output was translated to .axt format using the lavToAxt program and then to .psl format using the axtToPsl program. The axtSwap program was used to translate rn3-referenced chained blastz alignments to mm3 into mm3-referenced alignments to rn3. Blastz alignments were chained using the axtChain program. Chained alignments were processed into nets by the chainPreNet, chainNet, netSyntenic, and netClass programs. All programs run after blastz were written by Jim Kent at UCSC. ---------------------------------------------------------------- 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/mm3/vsRn3/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all files in the current directory) All files 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 (2002). 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 (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).