This directory contains alignments of the Fugu assembly (fr1, Aug. 2002) to the human assembly (hg17, May 2004). Files included in this directory: - axtTight directory: contains a highly conserved subset of the best alignments for any part of the human genome. - axtNet directory: contains chained and netted alignments, i.e. the best chains in the genome, with gaps in the best chains filled in by next-best chains where possible. - fugu.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html. - fugu.net.gz: "net" file that describes rearrangements between the species and the best Fugu match to any part of the human genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html. The alignments in the axtNet and axtTight directories are in "axt" format. For a description, see http://genome.ucsc.edu/goldenPath/help/axt.html. The alignments were produced by the blastz alignment program, which is available from Webb Miller's lab at Penn State University (http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix 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 400 and a gap extension penalty of 30. The minimum score for an alignment to be kept was 3000 for the first pass and 2200 for the second pass, which restricted the search space to the regions between two alignments found in the first pass. Each chromosome was divided into 10,000,000 base chunks with 10000 bases of overlap. The .lav format blastz output, which does not include the sequence, was converted to .axt with lavToAxt. The axtNet alignments were processed with chainNet, netSyntenic, and netClass 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/hg17/vsfr1/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) All the files in this directory are freely usable for any purpose. -------------------------------------------------------------------- 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. 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 Sep 30 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).