This directory contains alignments of the following assemblies: - target/reference: Rat (rn4, Nov. 2004 (Baylor 3.4/rn4), Baylor HGSC v. 3.4) - query: X. tropicalis (xenTro3, Nov. 2009 (JGI 4.2/xenTro3), US DOE Joint Genome Institute (JGI-PGF) (GCA_000004195.1)) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - rn4.xenTro3.all.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - rn4.xenTro3.net.gz: "net" file that describes rearrangements between the species and the best X. tropicalis match to any part of the Rat genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html . - axtNet/*.rn4.xenTro3.net.axt.gz: chained and netted alignments, i.e. the best chains in the Rat 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 rn4 and xenTro3 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 rn4 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 xenTro3, 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. The blastz scoring matrix (Q parameter) used was: A C G T A 91 -90 -25 -100 C -90 100 -100 -25 G -25 -100 100 -90 T -100 -25 -90 91 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=2200 for the first pass and L=8000 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: Y=3400 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 (loose): tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 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/rn4/vsXenTro3/. 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.