This directory contains alignments of the zebrafish genome (danRer1, May 2004) to the X. tropicalis assembly (xenTro1, Oct. 2004). Files included in this directory: - 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. - zebrafish.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html. - zebrafish.net.gz: "net" file that describes rearrangements between the species and the best zebrafish match to any part of the X. tropicalis 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 -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 10,000 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. Each chromosome was divided into 10,000,000 base chunks with 10,000 bases of overlap. The .lav format blastz output, which does not include the sequence, was converted to .axt with lavToAxt. 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/xenTro1/vsDanRer1. 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. Preliminary drafts of the X. tropicalis sequence are made freely available before scientific publication by the JGI and the X. tropicalis Genome Consortium, 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 (DOE Joint Genome Institute) is properly acknowledged. 3. Additional shotgun sequencing is ongoing, and future assembly releases will be made in a timely fashion. We expect to publish an initial analysis of a high quality draft X. tropicalis genome sequence in 2005 (with submission targeted for the spring of 2005) which will include descriptions of the large scale organization of the frog genome as well as genome-scale comparisons of the frog sequence and gene set with those of other animals. Others who would like to coordinate other genome-wide analysis with this work should contact Paul Richardson (firstname.lastname@example.org), JGI. We welcome a coordinated approach to describing this community resource. 4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - axtNet/ 2004-11-22 17:17 - md5sum.txt 2004-11-06 09:23 104 zebrafish.chain.gz 2004-11-06 09:01 382M zebrafish.net.gz 2004-11-06 09:02 42M