This directory contains alignments of the zebrafish assembly (danRer2, June 2004) to the Fugu assembly (fr1, Aug. 2002). Files included in this directory: - axtChrom directory: contains the axt alignments generated by blastz, in one file per chromosome. Blastz output was converted to lav format, which was then converted to axt format. - 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. - zebrafishDanRer2.chain.zip: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html. - zebrafishDanRer2.net.zip: "net" file that describes rearrangements between the species and the best zebrafish match to any part of the Fugu genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html. - md5sum.txt: checksums of the files in this directory The alignments in the axtNet directory 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 -114 -31 -123 C -114 100 -125 -31 G -31 -125 100 -114 T -123 -31 -114 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 3000 for the second pass, which restricted the search space to the regions between two alignments found in the first pass. The .lav format blastz output, which does not include the sequence, was converted to .axt with lavToAxt. Chains were produced by axtChain, 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. 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/fr1/vsDanRer2/. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) All the files in this directory are freely available for public use. The Zv4 zebrafish sequence data were produced by the Zebrafish Sequencing Group at the Sanger Institute and can be obtained directly from ftp://ftp.sanger.ac.uk/pub/zebrafish/. All sequence data are made available before scientific publication with the understanding that the groups involved in generating the data intend to publish the initial large-scale analyses of the dataset. This will include a summary detailing the data that have beeen generated and key features of the genome identified from genomic assembly and clone mapping/sequencing. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - axtChrom/ 2004-12-23 10:01 - md5sum.txt 2004-12-23 10:05 118 zebrafishDanRer2.chain.gz 2004-12-23 10:05 27M zebrafishDanRer2.net.gz 2004-12-23 10:05 8.0M