This directory contains the June 2007 assembly of the marmoset genome
(calJac1, WUSTL Callithrix_jacchus-2.0.2), as well as repeat annotations
and GenBank sequences.
This assembly was produced by the Genome Sequencing Center at the
Washington University School of Medicine in St. Louis.
For more information on the marmoset genome, see the project website:
Files included in this directory:
calJac1.2bit - contains the complete marmoset/calJac1 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
calJac1.agp.gz - Description of how the assembly was generated from
calJac1.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.
calJac1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
calJac1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. Repeat Masker version:
# May 17 2007 (open-3-1-8) version of RepeatMasker
Repeat Masker library version: RELEASE 20061006;
calJac1.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
est.fa.gz - Marmoset ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
calJac1.quals.fa.gz - quality scores in fasta file format
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Marmoset mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts for Xeno RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it could be slightly out
of sync with the Xeno RefSeq data which is updated daily for most
upstream2000.fa.gz - Same as upstream1000, but 2000 bases.
upstream5000.fa.gz - Same as upstream1000, but 5000 bases.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
calJac1.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 that 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/calJac1/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/calJac1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
Or with wget, all files:
With wget, a single file:
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
The Marmoset sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
2. Users are free to use the data in scientific papers analyzing these data
if the providers of these data are properly acknowledged. See
http://genome.ucsc.edu/goldenPath/credits.html for credit information.
It is requested that users of this marmoset sequence assembly acknowledge
the Washington University School of Medicine, Genome Sequencing Center
in any publications that result from use of this sequence assembly.
3. The centers producing the data reserve the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice.
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80