This directory contains alignments of the following assemblies: - target/reference: Human (hg18, Mar. 2006, NCBI Build 36.1) - query: Mouse (mm8, Feb 2006, NCBI Build 36) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - hg18.mm8.all.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - hg18.mm8.net.gz: "net" file that describes rearrangements between the species and the best Mouse match to any part of the Human genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html . - hg18.mm8.syn.net.gz: "syntenic net" file. This is the net filtered to remove non-syntenic alignments - axtNet/*.hg18.mm8.net.axt.gz: chained and netted alignments, i.e. the best chains in the Human 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 mm8-referenced chained blastz alignments to hg18 into hg18-referenced chains aligned to mm8. See the download directory goldenPath/mm8/vsHg18/README.txt for more information about the mm8-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. ---------------------------------------------------------------- To download a large file or multiple files from this directory, we recommend that you use ftp rather than downloading the files via our website. To do so: ftp hgdownload.cse.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/hg18/vsMm8 To download multiple files from the UNIX command line, use the "mget" command. mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) Use the "prompt" command to toggle the interactive mode if you do not want to be prompted for each file that you download. 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/ 2006-02-17 17:31 - md5sum.txt 2007-06-05 21:44 3.5K hg18.mm8.syn.net.gz 2006-05-03 20:12 187M hg18.mm8.net.gz 2006-02-17 17:15 196M hg18.mm8.all.chain.gz 2006-02-17 15:36 209M