This directory contains alignments of the human assembly (hg17, May 2004) to the Tetraodon assembly (tetNig1, Feb. 2004) 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 2000 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 for the blastz alignments and all repeats for each organism were used as lineage-specific repeats. Repeats were detected with Arian Smit's RepeatMasker program. The .lav format blastz output, which does not include the sequence, was converted to .axt with lavToAxt. ----------------------------------------------------------------- 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/vsHg17/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) All the tables in this directory are freely available for public use. 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.