This directory contains the Build 1 Version 1 (UCSC version panTro1) chimpanzee Arachne assembly produced by the Chimp Genome Sequencing Consortium. Files included in this directory: panTro1.2bit - contains the complete chimp/panTro1 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.zip - Description of how the chromosome-based assembly was generated, unpacking to one file per chromosome. chromFa.zip - 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.zip - 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.zip - RepeatMasker .out file for chromosomes, created with RepeatMasker at the -s sensitive setting. chromQuals.zip - Quality scores for all bases in the assembly, in one file per chromosome est.fa.gz - Chimp ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - checksum file mrna.fa.gz - Chimp mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. scaffolds.lft.zip - Offsets of scaffolds within chromosomes and their orientation on + or - strand, generated from the chromosome AGP files. 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. panTro1.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/panTro1/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 - chromAgp.zip 2004-02-12 15:30 941K chromFa.zip 2004-02-12 15:57 875M chromFaMasked.zip 2004-02-12 16:20 495M chromOut.zip 2004-02-03 13:55 146M chromQuals.zip 2004-07-06 20:44 466M est.fa.gz 2019-10-17 17:09 2.7M est.fa.gz.md5 2019-10-17 17:09 44 md5sum.txt 2014-02-03 10:24 340 mrna.fa.gz 2019-10-17 17:04 1.9M mrna.fa.gz.md5 2019-10-17 17:04 45 panTro1.2bit 2005-04-30 10:59 1.1G panTro1.chrom.sizes 2004-01-26 11:35 952 panTro1.fa.gz 2020-01-23 02:24 874M refMrna.fa.gz 2019-10-17 17:09 1.5M refMrna.fa.gz.md5 2019-10-17 17:09 48 scaffolds.lft.zip 2004-02-12 16:20 416K upstream1000.fa.gz 2019-10-17 17:10 3.2M upstream1000.fa.gz.md5 2019-10-17 17:10 53 upstream2000.fa.gz 2019-10-17 17:10 6.0M upstream2000.fa.gz.md5 2019-10-17 17:10 53 upstream5000.fa.gz 2019-10-17 17:11 14M upstream5000.fa.gz.md5 2019-10-17 17:11 53 xenoMrna.fa.gz 2016-02-27 07:59 5.0G xenoMrna.fa.gz.md5 2016-02-27 08:00 49 xenoRefMrna.fa.gz 2019-10-17 17:09 329M xenoRefMrna.fa.gz.md5 2019-10-17 17:09 52