This directory contains the Oct. 2010 (CGSC 2.1.3/panTro3) assembly of the chimp genome (panTro3, CGSC 2.1.3 (GCA_000001515.3)), as well as repeat annotations and GenBank sequences. This assembly was produced by Chimpanzee Sequencing and Analysis Consortium. For more information on the chimp genome, see the project website: http://genome.wustl.edu/genomes/view/pan_troglodytes/ Files included in this directory: panTro3.2bit - contains the complete chimp/panTro3 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 panTro3.agp.gz - Description of how the assembly was generated from fragments. panTro3.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. panTro3.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. panTro3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. RepeatMasker version: June 30 2010 (open-3-2-9) RepeatMasker library version: 20090604 panTro3.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. md5sum.txt - checksums of files in this directory 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. panTro3.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. panTro3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used - to construct the GC Percent track panTro3.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 panTro3.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 panTro3.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/panTro3/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - 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/panTro3/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro3/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/bigZips/chromFa.tar.gz' -O chromFa.tar.gz To unpack the *.tar.gz files: tar xvzf <file>.tar.gz To uncompress the fa.gz files: gunzip <file>.fa.gz The chimpanzee 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 - genes/ 2020-02-05 13:47 - est.fa.gz.md5 2019-10-17 16:29 44 mrna.fa.gz.md5 2019-10-17 16:14 45 refMrna.fa.gz.md5 2019-10-17 16:29 48 xenoMrna.fa.gz.md5 2019-10-17 16:25 49 xenoRefMrna.fa.gz.md5 2019-10-17 16:29 52 upstream1000.fa.gz.md5 2019-10-17 16:30 53 upstream2000.fa.gz.md5 2019-10-17 16:31 53 upstream5000.fa.gz.md5 2019-10-17 16:31 53 md5sum.txt 2019-01-17 15:57 479 panTro3.chrom.sizes 2011-02-17 14:20 654K panTro3.chromAlias.txt 2020-09-29 10:49 887K refMrna.fa.gz 2019-10-17 16:29 1.5M mrna.fa.gz 2019-10-17 16:14 1.9M est.fa.gz 2019-10-17 16:29 2.7M upstream1000.fa.gz 2019-10-17 16:30 3.9M panTro3.agp.gz 2011-02-23 13:11 4.4M panTro3.trf.bed.gz 2011-02-23 13:13 7.3M upstream2000.fa.gz 2019-10-17 16:31 7.4M panTro3.gc5Base.wig.gz 2019-01-17 14:52 12M upstream5000.fa.gz 2019-10-17 16:31 18M panTro3.fa.out.gz 2011-02-23 13:13 163M xenoRefMrna.fa.gz 2019-10-17 16:29 329M panTro3.fa.masked.gz 2011-02-23 13:36 479M panTro3.gc5Base.wib 2019-01-17 14:52 566M panTro3.2bit 2011-02-22 09:30 822M panTro3.fa.gz 2011-02-23 13:27 905M panTro3.gc5Base.wigVarStep.gz 2011-02-17 14:29 1.4G xenoMrna.fa.gz 2019-10-17 16:25 6.8G