This directory contains the May 2006 assembly of the chicken genome (galGal3, Chicken Genome Sequencing Consortium May 2006 release), as well as repeat annotations and GenBank sequences. This assembly was produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis. For more information on the chicken genome, see the project website: http://genome.wustl.edu/genome.cgi?GENOME=Gallus%20gallus Files included in this directory: galGal3.2bit - contains the complete chicken/galGal3 genome sequence in the 2bit file format. 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.tar.gz - Description of how the assembly was generated from fragments, unpacking to one file per chromosome. chromFa.tar.gz - 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. chromFaMasked.tar.gz - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.tar.gz - RepeatMasker .out files (one file per chromosome). RepeatMasker was run with the -s (sensitive) setting. The March 20 2006 (open-3-1-5) version of RepeatMasker and the library release 20060315 were used. chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into UCSC's BED format (one file per chromosome). est.fa.gz - Chicken ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. galGal3.quals.fa.gz - quality scores in fasta file format 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. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts for RefSeq genes with annotated 5' UTRs. This file is updated weekly so it could be slightly out of sync with the RefSeq data which is updated daily for most assemblies. upstream2000.zip - Same as upstream1000, but 2000 bases. upstream5000.zip - Same as upstream1000, but 5000 bases. 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. galGal3.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/galGal3/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 to the community by the Genome Sequencing Center, Washington University 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 these data if the providers of these data are properly cited: International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 9;432(7018):695-716. PMID: 15592404 See http://genome.ucsc.edu/goldenPath/credits.html for credit information. 3. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - chromAgp.tar.gz 2006-08-04 15:35 2.0M chromFa.tar.gz 2006-08-04 15:40 318M chromFaMasked.tar.gz 2006-08-04 15:44 283M chromOut.tar.gz 2006-08-04 15:35 15M chromTrf.tar.gz 2006-08-04 15:44 1.3M est.fa.gz 2020-02-28 03:20 142M est.fa.gz.md5 2020-02-28 03:20 44 galGal3.2bit 2006-05-15 08:55 267M galGal3.chrom.sizes 2006-05-15 17:24 947 galGal3.fa.gz 2020-01-23 02:22 318M galGal3.quals.fa.gz 2009-06-09 10:39 125M genes/ 2020-02-05 13:47 - md5sum.txt 2013-12-10 12:02 355 mrna.fa.gz 2020-02-28 03:05 12M mrna.fa.gz.md5 2020-02-28 03:05 45 refMrna.fa.gz 2020-02-28 03:21 5.3M refMrna.fa.gz.md5 2020-02-28 03:21 48 upstream1000.fa.gz 2020-02-28 03:21 1.4M upstream1000.fa.gz.md5 2020-02-28 03:21 53 upstream2000.fa.gz 2020-02-28 03:21 2.8M upstream2000.fa.gz.md5 2020-02-28 03:21 53 upstream5000.fa.gz 2020-02-28 03:21 6.8M upstream5000.fa.gz.md5 2020-02-28 03:21 53 xenoMrna.fa.gz 2020-02-28 03:15 6.8G xenoMrna.fa.gz.md5 2020-02-28 03:15 49 xenoRefMrna.fa.gz 2020-02-28 03:21 331M xenoRefMrna.fa.gz.md5 2020-02-28 03:21 52