This directory contains the Feb. 2004 assembly of the chicken genome (galGal2, Feb. 2004) from the Genome Sequencing Center at Washington University in St. Louis. Files included in this directory: galGal2.2bit - contains the complete chicken/galGal2 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 assembly was generated from fragments, unpacking to one file per chromosome. chromFa.zip - The assembly sequence in one file per chromosome. 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. RepeatMasker January 2004 version with RepBase libraries: RepBase Update 8.4, RM database version 20040225 chromFaMasked.zip - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.zip - RepeatMasker .out file for chromosomes. These were created by RepeatMasker at the -s sensitive setting. chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into one .bed file per chromosomes. est.fa.gz - Chicken ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - checksums of files in this directory mrna.fa.gz - Chicken mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. refMrna.fa.gz - RefSeq mRNA from the same species as the genome. 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. galGal2.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 that 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/galGal2/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) The chicken sequence is made freely available before scientific publication 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 are properly acknowledged. See http://genome.ucsc.edu/goldenPath/credits.html for credit information. 3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, 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 chromosome (that is, 30 Mb or more). 4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - chromAgp.zip 2004-02-25 13:29 2.7M chromFa.zip 2004-02-26 09:21 325M chromFaMasked.zip 2004-02-26 09:30 288M chromOut.zip 2004-02-25 21:44 16M chromTrf.zip 2004-02-25 13:50 1.4M est.fa.gz 2020-02-28 03:42 142M est.fa.gz.md5 2020-02-28 03:42 44 galGal2.2bit 2004-02-26 12:24 276M galGal2.chrom.sizes 2004-02-24 12:30 870 galGal2.fa.gz 2020-01-23 02:22 325M md5sum.txt 2014-05-05 15:32 329 mrna.fa.gz 2020-02-28 03:26 12M mrna.fa.gz.md5 2020-02-28 03:26 45 refMrna.fa.gz 2020-02-28 03:43 5.3M refMrna.fa.gz.md5 2020-02-28 03:43 48 upstream1000.fa.gz 2020-02-28 03:43 1.4M upstream1000.fa.gz.md5 2020-02-28 03:43 53 upstream2000.fa.gz 2020-02-28 03:43 2.7M upstream2000.fa.gz.md5 2020-02-28 03:43 53 upstream5000.fa.gz 2020-02-28 03:43 6.5M upstream5000.fa.gz.md5 2020-02-28 03:43 53 xenoMrna.fa.gz 2020-02-28 03:36 6.8G xenoMrna.fa.gz.md5 2020-02-28 03:36 49 xenoRefMrna.fa.gz 2020-02-28 03:42 331M xenoRefMrna.fa.gz.md5 2020-02-28 03:43 52