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.
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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 14:10 501K
ci1.chromAlias.txt 2022-09-08 14:10 70K
ci1.fa.gz 2020-01-23 02:20 35M
est.fa.gz 2019-10-16 22:38 250M
est.fa.gz.md5 2019-10-16 22:38 44
md5sum.txt 2014-05-05 16:14 290
mrna.fa.gz 2019-10-16 22:23 4.6M
mrna.fa.gz.md5 2019-10-16 22:23 45
refMrna.fa.gz 2019-10-16 22:39 711K
refMrna.fa.gz.md5 2019-10-16 22:39 48
xenoMrna.fa.gz 2019-10-16 22:33 6.8G
xenoMrna.fa.gz.md5 2019-10-16 22:34 49
xenoRefMrna.fa.gz 2019-10-16 22:39 330M
xenoRefMrna.fa.gz.md5 2019-10-16 22:39 52