This directory contains the Mar. 2005 freeze of the C. intestinalis genome (ci2) from the US DOE Joint Genome Institute (JGI). Files included in this directory: ci2.2bit - contains the complete C. intestinalis/ci2 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 ScaffoldFa.zip - The assembly sequence in one file per scaffold. 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. RepeatMasker version development-$Id: RepeatMasker,v 1.9 2005/05/04 18:27:42. ScaffoldFaMasked.zip - The assembly sequence in one file per scaffold. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. ScaffoldOut.zip - A single RepeatMasker .out file for scaffolds. These were created by RepeatMasker at the -s sensitive setting. ScaffoldTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and collected into one file. md5sum.txt - MD5 checksum of the previous four files to verify correct transmission. est.fa.gz - C. intestinalis ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. mrna.fa.gz - C. intestinalis 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. 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. ci2.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/ci2/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) The C. intestinalis sequence is made freely available by JGI. For restrictions on the use of these data, see the JGI Data Release Policy at http://genome.jgi-psf.org/ciona4/ciona4.download.html.
Name Last modified Size Description
Parent Directory - Scaffold.out.zip 2008-09-17 09:59 4.9M ScaffoldFa.zip 2008-09-17 10:01 44M ScaffoldFaMasked.zip 2008-09-17 10:02 37M ScaffoldTrf.zip 2008-09-17 10:02 1.2M ci2.2bit 2005-07-30 11:26 43M ci2.chrom.sizes 2005-10-11 08:50 82K ci2.fa.gz 2020-01-23 02:20 43M est.fa.gz 2019-10-15 15:01 250M est.fa.gz.md5 2019-10-15 15:01 44 md5sum.txt 2014-01-03 17:09 248 mrna.fa.gz 2019-10-15 14:48 4.6M mrna.fa.gz.md5 2019-10-15 14:48 45 refMrna.fa.gz 2019-10-15 15:02 711K refMrna.fa.gz.md5 2019-10-15 15:02 48 xenoMrna.fa.gz 2019-10-15 14:57 6.8G xenoMrna.fa.gz.md5 2019-10-15 14:57 49 xenoRefMrna.fa.gz 2019-10-15 15:02 330M xenoRefMrna.fa.gz.md5 2019-10-15 15:02 52