This directory contains the 25 Mar-2014 (Chlorocebus_sabeus 1.1/chlSab2) assembly of the
green monkey genome (chlSab2, Vervet Genomics Consortium GCA_000409795.2),
as well as repeat annotations and GenBank sequences.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/13136
http://www.ncbi.nlm.nih.gov/genome/assembly/132581
http://www.ncbi.nlm.nih.gov/bioproject/215854
Files included in this directory:
chlSab2.2bit - contains the complete green monkey/chlSab2 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
chlSab2.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
chlSab2.agp.gz - Description of how the assembly was generated from
fragments.
chlSab2.fa.gz - "Soft-masked" assembly sequence in one file.
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.
chlSab2.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
chlSab2.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
January 31 2015 (open-4-0-5) version of RepeatMasker
RepBase library: RELEASE 20140131
chlSab2.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
est.fa.gz - Green monkey ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Green monkey mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
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If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/chlSab2/bigZips. To download multiple files, use
the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/chlSab2/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/chlSab2/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/chlSab2/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/chlSab2/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
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GenBank Data Usage
The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
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Name Last modified Size Description
Parent Directory -
xenoRefMrna.fa.gz.md5 15-Jul-2017 06:40 52
xenoRefMrna.fa.gz 15-Jul-2017 06:40 301M
mrna.fa.gz.md5 15-Jul-2017 06:33 45
mrna.fa.gz 15-Jul-2017 06:33 214K
md5sum.txt 26-Mar-2015 15:35 358
est.fa.gz.md5 15-Jul-2017 06:40 44
est.fa.gz 15-Jul-2017 06:40 7.4M
chlSab2.trf.bed.gz 26-Mar-2015 15:17 7.8M
chlSab2.fa.out.gz 26-Mar-2015 15:17 161M
chlSab2.fa.masked.gz 26-Mar-2015 15:34 467M
chlSab2.fa.gz 26-Mar-2015 15:28 859M
chlSab2.chrom.sizes 08-Apr-2014 15:35 52K
chlSab2.agp.gz 26-Mar-2015 15:16 3.6M
chlSab2.2bit 10-Apr-2014 13:26 697M