This directory contains the Apr. 2012 (GeoFor_1.0/geoFor1) assembly of the medium ground finch genome
(geoFor1, Beijing Genomics Institute), 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/13302
http://www.ncbi.nlm.nih.gov/genome/assembly/402638
http://www.ncbi.nlm.nih.gov/bioproject/156703
Files included in this directory:
geoFor1.2bit - contains the complete medium ground finch/geoFor1 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
geoFor1.agp.gz - Description of how the assembly was generated from
fragments.
geoFor1.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.
geoFor1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
geoFor1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
April 26 2011 (open-3-3-0) version of RepeatMasker
RepBase library: RELEASE 20110920
geoFor1.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 - Medium ground finch mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
geoFor1.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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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/geoFor1/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/geoFor1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP \
rsync://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/bigZips/*'
With wget, a single file:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/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 -
mrna.fa.gz.md5 16-Jul-2017 00:33 45
xenoRefMrna.fa.gz.md5 16-Jul-2017 00:34 52
upstream1000.fa.gz.md5 16-Jul-2017 00:34 53
upstream2000.fa.gz.md5 16-Jul-2017 00:35 53
upstream5000.fa.gz.md5 16-Jul-2017 00:35 53
md5sum.txt 27-Jul-2012 14:51 304
mrna.fa.gz 16-Jul-2017 00:33 330
geoFor1.chrom.sizes 26-Jul-2012 16:08 356K
geoFor1.trf.bed.gz 27-Jul-2012 14:39 1.7M
upstream1000.fa.gz 16-Jul-2017 00:34 1.8M
geoFor1.agp.gz 27-Jul-2012 14:39 1.9M
upstream2000.fa.gz 16-Jul-2017 00:35 3.5M
upstream5000.fa.gz 16-Jul-2017 00:35 8.8M
geoFor1.fa.out.gz 27-Jul-2012 14:39 11M
geoFor1.fa.masked.gz 27-Jul-2012 14:49 276M
xenoRefMrna.fa.gz 16-Jul-2017 00:34 302M
geoFor1.2bit 26-Jul-2012 22:34 305M
geoFor1.fa.gz 27-Jul-2012 14:44 331M