This directory contains the Jan. 2010 (GGSC Nleu1.0/nomLeu1) assembly of the gibbon genome
(nomLeu1, GGSC (NCBI project 13975, accession GCA_000146795.1)), as well as repeat annotations and GenBank sequences.
This assembly was produced by the National Center for Biotechnology Information (NCBI).
For more information on the gibbon genome, see the project website:
http://www.ncbi.nlm.nih.gov/bioproject/13975
Files included in this directory:
nomLeu1.2bit - contains the complete gibbon/nomLeu1 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
nomLeu1.agp.gz - Description of how the assembly was generated from
fragments.
nomLeu1.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.
nomLeu1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
nomLeu1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. April 26 2011 (open-3-3-0) version of RepeatMasker
with RepeatMaskerLib.embl RELEASE 20110920
nomLeu1.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.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Gibbon mRNA from GenBank. 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.
nomLeu1.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
nomLeu1.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
nomLeu1.gc5Base.wig.gz - wiggle database table for the GC Percent track
- this is an older standard alternative to the current
- bigWig format of the track, sometimes usefull for analysis
nomLeu1.gc5Base.wib - binary data to correspond with the gc5Base.wig file
see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html
and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
for a discussion of how to use the wig.gz and .wib files for
interaction with the GC percent data values
nomLeu1.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
------------------------------------------------------------------
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/nomLeu1/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/nomLeu1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/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
Name Last modified Size Description
Parent Directory -
xenoMrna.fa.gz 2016-03-16 11:54 5.0G
nomLeu1.gc5Base.wigVarStep.gz 2010-10-29 15:42 1.4G
nomLeu1.fa.gz 2011-11-21 12:31 855M
nomLeu1.2bit 2010-10-31 16:50 731M
nomLeu1.gc5Base.wib 2019-01-17 14:51 540M
nomLeu1.fa.masked.gz 2011-11-21 12:41 454M
xenoRefMrna.fa.gz 2019-10-17 14:31 331M
nomLeu1.fa.out.gz 2011-11-21 12:17 152M
nomLeu1.gc5Base.wig.gz 2019-01-17 14:51 12M
nomLeu1.trf.bed.gz 2011-11-21 12:17 6.5M
nomLeu1.agp.gz 2011-11-21 12:16 4.7M
nomLeu1.chromAlias.bb 2022-09-08 14:14 2.8M
nomLeu1.chromAlias.txt 2022-09-08 14:14 429K
nomLeu1.chrom.sizes 2010-10-29 15:35 288K
mrna.fa.gz 2019-10-17 14:31 28K
md5sum.txt 2019-01-17 15:56 479
xenoRefMrna.fa.gz.md5 2019-10-17 14:31 52
xenoMrna.fa.gz.md5 2016-03-16 11:54 49
mrna.fa.gz.md5 2019-10-17 14:31 45
genes/ 2020-02-05 13:47 -