This directory contains the Dec. 2002 freeze of the C. intestinalis genome (ci1) from the US DOE Joint Genome Institute (JGI). Files included in this directory: ci1.2bit - contains the complete C. intestinalis/ci1 genome sequence in the 2bit file format. While we are providing the .2bit for this assembly, we will continue to use the .nib files in the Genome Browser. 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 January 2004 version with RepBase libraries: RepBase Update 8.4, RM database version 20040225. 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 - 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 translated into one .bed file per scaffold. est.fa.gz - C. intestinalis ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - MD5 checksum of these files to verify correct transmission. mrna.fa.gz - C. intestinalis mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. refMrna.zip - RefSeq mRNA from the same species as the genome. xenoMrna.zip - All GenBank mRNAs from species other than that of the genome. ci1.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. ci1.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 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/ci1/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 - ScaffoldFa.zip 2004-07-15 07:55 34M ScaffoldFaMasked.zip 2004-07-15 08:30 36M ScaffoldOut.zip 2004-07-15 08:27 4.9M ScaffoldTrf.zip 2004-07-15 07:58 506K ci1.2bit 2004-06-30 15:12 29M ci1.chrom.sizes 2012-02-28 16:11 47K ci1.chromAlias.bb 2022-09-08 22:08 501K ci1.chromAlias.txt 2022-09-08 22:08 70K ci1.fa.gz 2020-01-23 02:20 35M est.fa.gz 2020-02-27 21:04 250M est.fa.gz.md5 2020-02-27 21:04 44 md5sum.txt 2022-09-08 22:07 395 mrna.fa.gz 2020-02-27 20:49 4.6M mrna.fa.gz.md5 2020-02-27 20:49 45 refMrna.fa.gz 2020-02-27 21:04 711K refMrna.fa.gz.md5 2020-02-27 21:04 48 xenoMrna.fa.gz 2020-02-27 20:58 6.8G xenoMrna.fa.gz.md5 2020-02-27 20:59 49 xenoRefMrna.fa.gz 2020-02-27 21:04 336M xenoRefMrna.fa.gz.md5 2020-02-27 21:04 52