This directory contains the Build 2 Version 1 (UCSC version panTro2) chimpanzee 6X draft assembly produced by the Chimp Genome Sequencing Consortium. Files included in this directory: chromAgp.tar.gz - Description of how the chromosome-based assembly was generated, unpacking to one file per chromosome. chromFa.tar.gz - The working draft sequence 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. The main assembly is in the chrN.fa files where N is the name of the chromosome. The chrN_random.fa files contain clones which are either not yet finished, or which cannot be placed with certainty at a specific place on the chromosome. chromFaMasked.tar.gz - 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.tar.gz - RepeatMasker .out file for chromosomes, created with RepeatMasker at the -s sensitive setting. chromQuals.tar.gz - Quality scores for all bases in the assembly, in one file per chromosome. chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats with period of less than or equal to 12, and translated into one .bed file per chromosome. est.fa.gz - Chimp and human ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. panTro2.2bit - contains the complete chimp/panTro2 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 panTro2.quals.fa.gz - quality scores in fasta file format md5sum.txt - checksum file mrna.fa.gz - Chimp and human mRNA from GenBank. 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.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. panTro2.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/panTro2/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) 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 - panTro2.chrom.sizes 2006-03-06 10:31 921 panTro2.2bit 2006-03-24 14:05 832M chromAgp.tar.gz 2006-04-03 17:24 6.3M chromFa.tar.gz 2006-04-03 17:37 907M chromFaMasked.tar.gz 2006-04-03 17:44 494M chromOut.tar.gz 2006-04-03 17:45 156M chromTrf.tar.gz 2006-04-03 17:45 6.6M chromQuals.tar.gz 2006-07-17 15:33 416M panTro2.quals.fa.gz 2009-06-08 11:42 72M md5sum.txt 2009-06-10 10:24 566 mrna.fa.gz 2020-02-28 14:48 1.9M mrna.fa.gz.md5 2020-02-28 14:48 45 xenoMrna.fa.gz 2020-02-28 14:57 6.8G xenoMrna.fa.gz.md5 2020-02-28 14:58 49 est.fa.gz 2020-02-28 15:02 2.7M est.fa.gz.md5 2020-02-28 15:02 44 xenoRefMrna.fa.gz 2020-02-28 15:02 335M xenoRefMrna.fa.gz.md5 2020-02-28 15:02 52 refMrna.fa.gz 2020-02-28 15:03 1.5M refMrna.fa.gz.md5 2020-02-28 15:03 48 upstream1000.fa.gz 2020-02-28 15:03 491K upstream1000.fa.gz.md5 2020-02-28 15:03 53 upstream2000.fa.gz 2020-02-28 15:03 931K upstream2000.fa.gz.md5 2020-02-28 15:03 53 upstream5000.fa.gz 2020-02-28 15:03 2.2M upstream5000.fa.gz.md5 2020-02-28 15:03 53