This directory contains alignments of the following assemblies: - target/reference: Marmoset (calJac1, Jun. 2007, Callithrix_jacchus-WUSTL 2.0.2) - query: Orangutan (ponAbe2, Jul. 2007, WUSTL 3.0) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - calJac1.ponAbe2.all.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - calJac1.ponAbe2.net.gz: "net" file that describes rearrangements between the species and the best Orangutan match to any part of the Marmoset genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html . - calJac1.ponAbe2.net.axt.gz: chained and netted alignments, i.e. the best chains in the Marmoset 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 ponAbe2-referenced chained blastz alignments to calJac1 into calJac1-referenced chains aligned to ponAbe2. See the download directory goldenPath/ponAbe2/vsCalJac1/README.txt for more information about the ponAbe2-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/calJac1/vsPonAbe2/. 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, 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).