This directory contains alignments of the following assemblies: - target/reference: Human (hg18, Mar. 2006, NCBI Build 36.1) - query: Chimp (panTro2, Jan. 2006, Washington University Build 2 Version 1) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - hg18.panTro2.all.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - hg18.panTro2.net.gz: "net" file that describes rearrangements between the species and the best Chimp match to any part of the Human genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html . - hg18.panTro2.rbest.net.gz: "net" file containing only reciprocal best alignment chains. This is produced by extracting the chains from the panTro2.hg18 alignment net and then netting these with hg18 as the target, so that only the best human alignments to chimp that are also the best in human are retained. - hg18.panTro2.rbest.chain.gz: reciprocal best chained blastz alignments. These chains are extracted from the reciprocal best net file. - axtNet/*.hg18.panTro2.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 . - axtRBestNet/*.hg18.panTro2.net.axt.gz: reciprocal best chained and netted alignments, i.e. the best chains in the Human genome that are also the best matches in the Chimp genome. These are obtained from the reciprocal best chains. The chainSwap program was used to translate panTro2-referenced chained blastz alignments to hg18 into hg18-referenced chains aligned to panTro2. See the download directory goldenPath/panTro2/vsHg18/README.txt for more information about the panTro2-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: go to the directory goldenPath/hg18/vsPanTro2 To download multiple files from the UNIX command line, use the "mget" command. mget ... - 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. Genome Res. 13(1), 103-7 (2003).