This directory contains alignments of the following assemblies: - target/reference: Zebrafish (danRer3, May 2005, Sanger Centre, Danio rerio Sequencing Project Zv5) - query: Tetraodon (tetNig1, Feb. 2004, Genoscope and Broad Institute, V7) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - danRer3.tetNig1.all.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - danRer3.tetNig1.net.gz: "net" file that describes rearrangements between the species and the best Tetraodon match to any part of the Zebrafish genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html . - axtNet/*.danRer3.tetNig1.net.axt.gz: chained and netted alignments, i.e. the best chains in the Zebrafish 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 danRer3 and tetNig1 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 danRer3 sequences larger than 505,000 bases were split into chunks of 505,000 bases overlapping by 5,000 bases for alignment. A similar process was followed for tetNig1, with chunks of 1000,000,000 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. Because the danRer3 chrNA and chrUn chromosomes and the tetNig1 random chromosomes are comprised of unordered scaffolds separated by 500 <em>N</em>s and 1000 <em>N</em>s respectively, the blastz alignments and subsequent chaining were first performed on the scaffolds, and the coordinates were then lifted up to the chromosome level. This avoided false alignments across the <em>N</em>s. The M parameter was set to utilize the Blastz dynamic masking functionality. The tetraodon sequence was split into 500 kb contigs for the non-random chromosomes (lifted up to the chromosome level after chaining) and scaffolds for the random chromosomes. Each chunk of danRer3 sequence was aligned with all of the tetNig1 sequence in order for dynamic masking to occur. 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=3000 for the first pass and L=2200 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=2500. Other blastz parameters specifically set for this species pair: M=50 The .lav format blastz output was translated to the .psl format with lavToPsl, then chained by the axtChain program. 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/danRer3/vsTetNig1/. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all files in the current directory) All files in this directory are freely available for public use. -------------------------------------------------------------------- References 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</A>. Genome Res. 13(1), 103-7 (2003).
Name Last modified Size Description
Parent Directory - axtNet/ 2005-11-17 11:21 - danRer3.tetNig1.all.chain.gz 2005-11-15 13:47 40M danRer3.tetNig1.net.gz 2005-11-16 09:09 18M md5sum.txt 2005-11-17 11:23 2.2K