This directory contains alignments of the following assemblies: - target/reference: Mouse (mm10, Dec. 2011 (GRCm38/mm10), Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)) - query: Rat (rn5, Mar. 2012 (RGSC 5.0/rn5), RGSC Rnor_5.0 (GCA_000001895.3)) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - mm10.rn5.all.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - mm10.rn5.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 . - axtNet/*.mm10.rn5.net.axt.gz: chained and netted alignments, i.e. the best chains in the Mouse genome, with gaps in the best chains filled in by next-best chains where possible. The axt format is described in http://genome.ucsc.edu/goldenPath/help/axt.html . The mm10 and rn5 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 mm10 sequences larger than 20,010,000 bases were split into chunks of 20,010,000 bases overlapping by 10,000 bases for alignment. A similar process was followed for rn5, with chunks of 10,000,000 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 Rat/Mouse 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: A C G T A 100 -139 -54 -170 C -139 95 -83 -54 G -54 -83 95 -139 T -170 -54 -139 100 with a gap open penalty of O=600 and a gap extension penalty of E=55. The minimum score for an alignment to be kept was K=3000 for the first pass and L=3000 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. Other blastz parameters specifically set for this species pair: E=55 O=600 T=2 Y=5000 The .lav format blastz output was translated to the .psl format with lavToPsl, then chained by the axtChain program. Chain minimum score: 5000, and linearGap matrix of (medium): tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Chained alignments were processed into nets by the chainNet, netSyntenic, and netClass programs. Best-chain alignments in axt format were extracted by the netToAxt program. 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/mm10/vsRn5/. 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 VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002;:115-26. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7.