This directory contains alignments of the following assemblies: - target/reference: Stickleback (gasAcu1, Feb. 2006 (Broad/gasAcu1), Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000)) - query: Zebrafish (danRer7, Jul. 2010 (Zv9/danRer7), Wellcome Trust Sanger Institute Zv9 (GCA_000002035.2)) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - gasAcu1.danRer7.all.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - gasAcu1.danRer7.net.gz: "net" file that describes rearrangements between the species and the best Zebrafish match to any part of the Stickleback genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html . - axtNet/*.gasAcu1.danRer7.net.axt.gz: chained and netted alignments, i.e. the best chains in the Stickleback 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 chainSwap program was used to translate danRer7-referenced chained blastz alignments to gasAcu1 into gasAcu1-referenced chains aligned to danRer7. See the download directory goldenPath/danRer7/vsGasAcu1/README.txt for more information about the danRer7-referenced blastz and chaining process. 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/gasAcu1/vsDanRer7/. 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 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.
Name Last modified Size Description
Parent Directory - axtNet/ 2010-12-17 15:04 - md5sum.txt 2010-12-17 15:04 1.8K gasAcu1.danRer7.net.gz 2010-12-17 14:59 22M gasAcu1.danRer7.all.chain.gz 2010-12-17 14:41 232M