This directory contains alignments of the Fugu assembly (fr1, Aug. 2002) to the zebrafish assembly (danRer1, Nov. 2003) 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. --------------------------------------------------------------- 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/danRer1/fr1/. 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 available for public use. The Zv3 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.