This directory contains the Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) assembly of the chicken genome (galGal4, ICGSC Gallus_gallus-4.0 (GCA_000002315.2)), as well as repeat annotations and GenBank sequences. For more information about this assembly, please note the NCBI resources: http://www.ncbi.nlm.nih.gov/genome/111 http://www.ncbi.nlm.nih.gov/genome/assembly/317958 http://www.ncbi.nlm.nih.gov/bioproject/13342 Files included in this directory: galGal4.2bit - contains the complete chicken/galGal4 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 galGal4.agp.gz - Description of how the assembly was generated from fragments. galGal4.fa.gz - "Soft-masked" assembly sequence in one file. 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. galGal4.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. galGal4.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. April 26 2011 (open-3-3-0) version of RepeatMasker, RepeatMaskerLib.embl version: CC RELEASE 20110920 galGal4.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into UCSC's BED format. 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. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts of RefSeq genes with annotated 5' UTRs. This file is updated weekly so it might be slightly out of sync with the RefSeq data which is updated daily for most assemblies. upstream2000.fa.gz - Same as upstream1000, but 2000 bases. upstream5000.fa.gz - 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. galGal4.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. galGal4.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used - to construct the GC Percent track galGal4.gc5Base.wig.gz - wiggle database table for the GC Percent track - this is an older standard alternative to the current - bigWig format of the track, sometimes usefull for analysis galGal4.gc5Base.wib - binary data to correspond with the gc5Base.wig file see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database for a discussion of how to use the wig.gz and .wib files for interaction with the GC percent data values galGal4.chromAlias.txt - sequence name alias file, one line for each sequence name. First column is sequence name followed by tab separated alias names. ------------------------------------------------------------------ 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 [username: anonymous, password: your email address], then cd to the directory goldenPath/galGal4/bigZips. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) Alternate methods to ftp access. Using an rsync command to download the entire directory: rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal4/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal4/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/bigZips/chromFa.tar.gz' -O chromFa.tar.gz To unpack the *.tar.gz files: tar xvzf .tar.gz To uncompress the fa.gz files: gunzip .fa.gz ------------------------------------------------------------------ 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. ------------------------------------------------------------------