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
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
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
ci1.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/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.
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80