This directory contains a dump of the UCSC genome annotation database for
the Jul. 2008 (Broad/vicPac1) assembly of the alpaca genome (vicPac1, Broad Institute vicPac1).
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/905
http://www.ncbi.nlm.nih.gov/genome/assembly/199718
http://www.ncbi.nlm.nih.gov/bioproject/30567
Files included in this directory (updated nightly):
- *.sql files: the MySQL commands used to create the tables
- *.txt.gz files: the database tables in a tab-delimited format
compressed with gzip.
To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
http://genome.ucsc.edu/cgi-bin/hgTables?db=vicPac1
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
---------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend 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/vicPac1/database/. 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/vicPac1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/vicPac1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/vicPac1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/vicPac1/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
To uncompress the *.txt.gz files:
gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.
To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql vicPac1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql vicPac1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
-----------------------------------------------------------------------------
The Alpaca 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 provider of these data (The Broad Institute) is
properly acknowledged.
3. The center producing the data reserves 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. 1. The data may
be freely downloaded, used in analyses, and repackaged in databases.
-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
-----------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
all_est.sql 15-May-2016 11:43 2.1K
all_est.txt.gz 15-May-2016 11:43 43K
augustusGene.sql 26-Jul-2015 17:28 1.9K
augustusGene.txt.gz 26-Jul-2015 17:28 1.4M
bigFiles.sql 02-Jul-2017 13:34 1.4K
bigFiles.txt.gz 02-Jul-2017 13:34 33
chainBosTau7.sql 16-Nov-2012 13:16 1.7K
chainBosTau7.txt.gz 16-Nov-2012 13:17 921M
chainBosTau7Link.sql 16-Nov-2012 12:57 1.6K
chainBosTau7Link.txt.gz 16-Nov-2012 13:03 3.2G
chainMm10.sql 16-Nov-2012 13:24 1.7K
chainMm10.txt.gz 16-Nov-2012 13:24 42M
chainMm10Link.sql 16-Nov-2012 13:22 1.5K
chainMm10Link.txt.gz 16-Nov-2012 13:22 329M
chromInfo.sql 16-Nov-2012 12:57 1.4K
chromInfo.txt.gz 16-Nov-2012 12:57 867K
cpgIslandExt.sql 16-Nov-2012 13:21 1.7K
cpgIslandExt.txt.gz 16-Nov-2012 13:21 463K
cpgIslandExtUnmasked.sql 01-Jun-2014 20:17 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 20:17 511K
cytoBandIdeo.sql 28-Apr-2013 22:41 1.5K
cytoBandIdeo.txt.gz 28-Apr-2013 22:41 928K
ensGene.sql 14-Sep-2015 11:04 1.9K
ensGene.txt.gz 14-Sep-2015 11:04 1.4M
ensGtp.sql 14-Sep-2015 11:05 1.4K
ensGtp.txt.gz 14-Sep-2015 11:05 135K
ensPep.sql 14-Sep-2015 11:05 1.3K
ensPep.txt.gz 14-Sep-2015 11:05 3.2M
ensemblGeneScaffold.sql 14-Sep-2015 11:05 1.7K
ensemblGeneScaffold.txt.gz 14-Sep-2015 11:05 4.8M
ensemblSource.sql 14-Sep-2015 11:04 1.4K
ensemblSource.txt.gz 14-Sep-2015 11:04 41K
ensemblToGeneName.sql 14-Sep-2015 11:04 1.4K
ensemblToGeneName.txt.gz 14-Sep-2015 11:04 85K
estOrientInfo.sql 15-May-2016 11:44 1.8K
estOrientInfo.txt.gz 15-May-2016 11:44 15K
gap.sql 16-Nov-2012 13:24 1.7K
gap.txt.gz 16-Nov-2012 13:24 5.1M
gbLoaded.sql 25-Jun-2017 22:29 1.6K
gbLoaded.txt.gz 25-Jun-2017 22:29 11K
gc5Base.sql 16-Nov-2012 13:21 1.9K
gc5Base.txt.gz 16-Nov-2012 13:21 15M
genscan.sql 16-Nov-2012 12:57 1.7K
genscan.txt.gz 16-Nov-2012 12:57 3.0M
gold.sql 16-Nov-2012 12:57 1.8K
gold.txt.gz 16-Nov-2012 12:57 8.5M
grp.sql 02-Mar-2014 04:18 1.4K
grp.txt.gz 02-Mar-2014 04:18 208
hgFindSpec.sql 02-Jul-2017 13:34 1.7K
hgFindSpec.txt.gz 02-Jul-2017 13:34 557
history.sql 16-Nov-2012 12:57 1.6K
history.txt.gz 16-Nov-2012 12:57 1.0K
intronEst.sql 15-May-2016 11:43 2.1K
intronEst.txt.gz 15-May-2016 11:43 3.7K
microsat.sql 24-Aug-2015 02:53 1.5K
microsat.txt.gz 24-Aug-2015 02:53 170K
nestedRepeats.sql 16-Nov-2012 12:56 2.1K
nestedRepeats.txt.gz 16-Nov-2012 12:56 6.4M
netBosTau7.sql 16-Nov-2012 13:21 2.1K
netBosTau7.txt.gz 16-Nov-2012 13:22 56M
netMm10.sql 16-Nov-2012 12:56 2.1K
netMm10.txt.gz 16-Nov-2012 12:56 47M
quality.sql 16-Nov-2012 13:23 1.9K
quality.txt.gz 16-Nov-2012 13:24 59M
rmsk.sql 16-Nov-2012 13:21 2.1K
rmsk.txt.gz 16-Nov-2012 13:21 68M
simpleRepeat.sql 16-Nov-2012 13:21 2.1K
simpleRepeat.txt.gz 16-Nov-2012 13:21 11M
tableDescriptions.sql 02-Jul-2017 13:34 1.4K
tableDescriptions.txt.gz 02-Jul-2017 13:34 4.6K
tableList.sql 02-Jul-2017 13:34 1.5K
tableList.txt.gz 02-Jul-2017 13:34 2.5K
trackDb.sql 02-Jul-2017 13:34 2.0K
trackDb.txt.gz 02-Jul-2017 13:34 21K
windowmaskerSdust.sql 16-Nov-2012 13:20 1.5K
windowmaskerSdust.txt.gz 16-Nov-2012 13:20 96M
xenoRefFlat.sql 25-Jun-2017 22:28 1.7K
xenoRefFlat.txt.gz 25-Jun-2017 22:28 25M
xenoRefGene.sql 25-Jun-2017 22:27 1.9K
xenoRefGene.txt.gz 25-Jun-2017 22:27 28M
xenoRefSeqAli.sql 25-Jun-2017 22:29 2.1K
xenoRefSeqAli.txt.gz 25-Jun-2017 22:29 27M