This directory contains alignments of the Fugu assembly (fr1, Aug. 2002) to the Tetraodon assembly (tetNig1, Feb. 2004). 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. - fr1.chain.zip: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html. - fr1.net.zip: "net" file that describes rearrangements between the species and the best Fugu match to any part of the Tetraodon 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 8000 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 10,010,000 base chunks for the blastz alignments. The .lav format blastz output, which does not include the sequence, was converted to .axt with lavToAxt. There are no lineage-specific repeats available for these two fish; therefore, none were used in the blastz alignments. ---------------------------------------------------------------- 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/tetNig1/vsFr1/. 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 usable for any purpose. The Tetraodon sequence has been freely provided by Genoscope before publication for use in the UCSC Genome Browser 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, provided that the Genoscope is properly acknowledged. 3. Genoscope reserves the right to publish the initial large-scale analyses of the dataset, 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 Tetraodon chromosome (that is, 5 Mb or more). 4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - axtChrom/ 2004-12-02 13:58 - fr1.chain.zip 2004-09-08 14:24 34M fr1.net.zip 2004-09-08 14:33 24M md5sum.txt 2004-09-08 14:33 94