This directory contains the Apr. 2004 freeze of the D. yakuba genome (droYak1) from the Genome Sequencing Center at Washington University School of Medicine in St. Louis. Files included in this directory: droYak1.2bit - contains the complete D. yakuba/droYak1 genome sequence in the 2bit file format. While we are providing the .2bit for this assembly, we will continue to use the .nib files in the Genome Browser. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. The utility program, twoBitToFa (available from the kent src tree), can be used to extract .fa file(s) from this file. A pre-compiled version of the command line tool can be found at: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ See also: http://genome.ucsc.edu/admin/git.html http://genome.ucsc.edu/admin/jk-install.html chromAgp.zip - Description of how the working draft was generated from fragments at a chromosome layout level. chromFa.zip - The working draft sequence chromosome in one file per chromosome. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are in lower case while non-repeating sequence is in upper case. RepeatMasker March 2004 version with RepBase libraries: RepBase Update 8.4, RM database version 20040225 chromFaMasked.zip - The working draft sequence in one file per chromosome. Repeats are masked by capital N's and non-repeating sequence is shown in upper case. chromOut.zip - RepeatMasker .out file for chromosomes. These were done with RepeatMasker at the -s sensitive setting. chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, translated into one .bed file per chromosomes. est.fa.gz - D. yakuba ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. ms5sum.txt - Checksums of files in this directory. mrna.fa.gz - D. yakuba mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. xenoMrna.fa.gz - GenBank mRNAs from species other than that of the genome. This sequence data is updated once a week via automatic GenBank updates. droYak1.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. ------------------------------------------------------------------------ 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/droYak1/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) The D. yakuba sequence is made freely available before scientific publication by The Genome Sequencing Center, WUSTL School of Medicine 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 providers of these data (Genome Sequencing Center, WUSTL School of Medicine) are properly acknowledged. 3. The Drosophila yakuba analysis group is aiming to publish an initial analysis of the D. yakuba genome sequence in 2005 (submitted in early 2005) that will include descriptions of the assembly, genome landscape, comparative analysis and initial gene content. People who would like to coordinate other genome-wide analysis with this work should contact Richard K. Wilson, Genome Sequencing Center Director, Washington University School of Medicine. 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 - chromAgp.zip 2004-05-21 23:59 597K chromFa.zip 2004-05-22 00:00 52M chromFaMasked.zip 2004-05-22 00:02 43M chromOut.zip 2004-05-21 23:59 4.3M chromTrf.zip 2004-05-22 00:02 693K droYak1.2bit 2004-05-21 23:51 44M droYak1.chrom.sizes 2004-05-21 18:07 310 droYak1.fa.gz 2020-01-23 02:21 52M est.fa.gz 2020-02-28 00:37 1.6M est.fa.gz.md5 2020-02-28 00:37 44 md5sum.txt 2014-05-05 16:19 286 mrna.fa.gz 2020-02-28 00:33 175K mrna.fa.gz.md5 2020-02-28 00:33 45 xenoMrna.fa.gz 2016-03-14 20:21 5.0G xenoMrna.fa.gz.md5 2016-03-14 20:21 49 xenoRefMrna.fa.gz 2020-02-28 00:37 337M xenoRefMrna.fa.gz.md5 2020-02-28 00:37 52