This directory contains the Feb. 2006 assembly of the stickleback genome
(gasAcu1, Broad Institute version 1.0), as well as repeat annotations and
GenBank sequences.
This assembly was produced by the Broad Institute at MIT and Harvard.
For more information on the stickleback genome, see the project website:
http://www.broad.mit.edu/tools/data/data-vert.html
Files included in this directory:
gasAcu1.2bit - contains the complete stickleback/gasAcu1 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
chromAgp.tar.gz - Description of how the assembly was generated from
fragments, unpacking to one file per chromosome.
chromFa.tar.gz - The assembly sequence in one file per chromosome.
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.
chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
RepeatMasker was run with the -s (sensitive) setting.
The March 20 2006 (open-3-1-5) version of RepeatMasker and library
release 20060315 were used.
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format (one file per chromosome).
gasAcu1.quals.fa.gz - quality scores in fasta file format
md5sum.txt - checksums of files in this directory
gasAcu1.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
gasAcu1.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 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/gasAcu1/bigZips. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
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The stickleback sequence is made freely available before scientific
publication with the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing particular
genes and regions if the providers of these data (The Broad Institute) are
properly acknowledged.
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.
Name Last modified Size Description
Parent Directory -
genes/ 2020-02-05 13:47 -
est.fa.gz.md5 2019-10-15 20:06 44
mrna.fa.gz.md5 2019-10-15 19:50 45
refMrna.fa.gz.md5 2019-10-15 20:06 48
xenoMrna.fa.gz.md5 2019-10-15 20:01 49
xenoRefMrna.fa.gz.md5 2019-10-15 20:06 52
upstream1000.fa.gz.md5 2019-10-15 20:06 53
upstream2000.fa.gz.md5 2019-10-15 20:06 53
upstream5000.fa.gz.md5 2019-10-15 20:06 53
gasAcu1.chromAlias.txt 2022-09-08 14:12 343
gasAcu1.chrom.sizes 2006-08-15 23:46 354
md5sum.txt 2014-01-03 16:15 355
gasAcu1.chromAlias.bb 2022-09-08 14:12 33K
refMrna.fa.gz 2019-10-15 20:06 39K
chromAgp.tar.gz 2006-08-16 13:09 446K
chromTrf.tar.gz 2006-08-16 13:14 1.4M
mrna.fa.gz 2019-10-15 19:50 1.5M
upstream1000.fa.gz 2019-10-15 20:06 2.2M
upstream2000.fa.gz 2019-10-15 20:06 4.2M
chromOut.tar.gz 2006-08-16 13:09 4.6M
upstream5000.fa.gz 2019-10-15 20:06 10M
gasAcu1.quals.fa.gz 2009-06-09 10:38 38M
est.fa.gz 2019-10-15 20:06 108M
gasAcu1.2bit 2006-08-16 12:43 112M
chromFaMasked.tar.gz 2006-08-16 13:14 131M
chromFa.tar.gz 2006-08-16 13:12 134M
gasAcu1.fa.gz 2020-01-23 02:22 134M
xenoRefMrna.fa.gz 2019-10-15 20:06 331M
xenoMrna.fa.gz 2019-10-15 20:01 6.8G