This directory contains alignments of the chicken assembly (galGal2, Feb. 2004) to the opossum assembly (monDom1, Oct. 2004). Files included in this directory: - chicken.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html. - chicken.net.gz: "net" file that describes rearrangements between the species and the best chicken match to any part of the opossum genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.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 5,000 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. Extra blastz parameters: H=2000 interpolate between alignments at threshold K = 2000. K=2200 threshold for MSPs. L=10000 threshold for gapped alignments. Y=3400 X-drop parameter for gapped extension. Each chromosome or scaffold was divided into 10,000,000 base chunks for the blastz alignments. No lineage specific repeats were used in these alignments. The .lav format blastz output, which does not include the sequence, was converted to .axt with lavToAxt. Low scores can occur using the scoring matrix above and with repeats abridged; therefore, alignments were rescored using PSU's restore_rpts program and the default scoring matrix: A C G T A 91 -114 -31 -123 C -114 100 -125 -31 G -31 -125 100 -114 T -123 -31 -114 91 For chaining, the axtChain linearGap option was used to specify gap penalties: tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Chains produced by axtChain were also filtered with a minimum score of 5000 and then chainAntiRepeat was applied to remove chains that are primarily the result of repeats and degenerate DNA. ---------------------------------------------------------------- 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/monDom1/vsGalGal2/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) Preliminary drafts of the opossum sequence are made freely available before scientific publication by the Broad Institute, with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of this data (The Broad Institute) is properly acknowledged. 3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). 4. Any redistribution of the data should carry this notice. -------------------------------------------------------------------- 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).