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.
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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/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 -
ci2.2bit 2005-07-30 11:26 43M
ci2.chrom.sizes 2005-10-11 08:50 82K
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
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
xenoMrna.fa.gz 2019-10-15 14:57 6.8G
xenoMrna.fa.gz.md5 2019-10-15 14:57 49
est.fa.gz 2019-10-15 15:01 250M
est.fa.gz.md5 2019-10-15 15:01 44
xenoRefMrna.fa.gz 2019-10-15 15:02 330M
xenoRefMrna.fa.gz.md5 2019-10-15 15:02 52
refMrna.fa.gz 2019-10-15 15:02 711K
refMrna.fa.gz.md5 2019-10-15 15:02 48
ci2.fa.gz 2020-01-23 02:20 43M