This directory contains a dump of the UCSC genome annotation database for
the Nov. 2011 (Broad/speTri2) assembly of the squirrel genome (speTri2,
Broad Institute (GCA_000236235.1)). 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/472
http://www.ncbi.nlm.nih.gov/genome/assembly/317808
http://www.ncbi.nlm.nih.gov/bioproject/61725
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=speTri2
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
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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/speTri2/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/speTri2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/speTri2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/speTri2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/speTri2/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 speTri2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql speTri2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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The Squirrel 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.
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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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All the files and tables in this directory are freely usable for any purpose.
-----------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
all_est.sql 2012-11-13 11:20 2.1K
all_est.txt.gz 2012-11-13 11:20 263K
all_mrna.sql 2020-08-20 11:08 2.1K
all_mrna.txt.gz 2020-08-20 11:08 5.2K
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 2.2M
bigFiles.sql 2024-11-17 03:41 1.4K
bigFiles.txt.gz 2024-11-17 03:41 94
chainMm10.sql 2012-11-13 11:21 1.7K
chainMm10.txt.gz 2012-11-13 11:21 89M
chainMm10Link.sql 2012-11-13 11:17 1.5K
chainMm10Link.txt.gz 2012-11-13 11:18 618M
chainMm39.sql 2020-11-26 01:15 1.7K
chainMm39.txt.gz 2020-11-26 01:15 72M
chainMm39Link.sql 2020-11-26 01:20 1.6K
chainMm39Link.txt.gz 2020-11-26 01:20 558M
chromAlias.sql 2018-02-18 08:40 1.4K
chromAlias.txt.gz 2018-02-18 08:40 113K
chromInfo.sql 2012-11-13 11:22 1.4K
chromInfo.txt.gz 2012-11-13 11:22 58K
cpgIslandExt.sql 2012-11-13 11:22 1.7K
cpgIslandExt.txt.gz 2012-11-13 11:22 564K
cpgIslandExtUnmasked.sql 2014-06-01 19:49 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 19:49 596K
cytoBandIdeo.sql 2013-04-28 21:49 1.5K
cytoBandIdeo.txt.gz 2013-04-28 21:49 61K
ensGene.sql 2021-05-25 14:48 1.9K
ensGene.txt.gz 2021-05-25 14:48 2.4M
ensGtp.sql 2021-05-25 14:48 1.4K
ensGtp.txt.gz 2021-05-25 14:48 337K
ensPep.sql 2021-05-25 14:50 1.3K
ensPep.txt.gz 2021-05-25 14:50 8.5M
ensemblSource.sql 2021-05-25 14:50 1.4K
ensemblSource.txt.gz 2021-05-25 14:50 100K
ensemblToGeneName.sql 2021-05-25 14:48 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:48 161K
estOrientInfo.sql 2012-11-13 11:22 1.8K
estOrientInfo.txt.gz 2012-11-13 11:22 69K
extNcbiRefSeq.sql 2020-05-10 03:29 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:29 91
gap.sql 2012-11-13 11:23 1.6K
gap.txt.gz 2012-11-13 11:23 1.8M
gbLoaded.sql 2020-08-20 11:38 1.6K
gbLoaded.txt.gz 2020-08-20 11:38 87K
gc5BaseBw.sql 2012-11-13 11:20 1.3K
gc5BaseBw.txt.gz 2012-11-13 11:20 63
genscan.sql 2012-11-13 11:22 1.7K
genscan.txt.gz 2012-11-13 11:22 3.0M
gold.sql 2012-11-13 11:22 1.7K
gold.txt.gz 2012-11-13 11:22 2.4M
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 1.2K
history.sql 2012-11-13 11:22 1.6K
history.txt.gz 2012-11-13 11:22 560
intronEst.sql 2012-11-13 11:22 2.1K
intronEst.txt.gz 2012-11-13 11:22 137K
microsat.sql 2015-08-24 01:44 1.5K
microsat.txt.gz 2015-08-24 01:44 833K
mrnaOrientInfo.sql 2020-08-20 11:08 1.8K
mrnaOrientInfo.txt.gz 2020-08-20 11:08 1.3K
ncbiRefSeq.sql 2020-05-10 03:29 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:29 2.6M
ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:29 260K
ncbiRefSeqCurated.sql 2020-05-10 03:29 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:29 3.2K
ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:29 1.2M
ncbiRefSeqOther.sql 2020-05-10 03:29 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:29 75
ncbiRefSeqPepTable.sql 2020-05-10 03:29 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:29 9.0M
ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 2.6M
ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 3.3M
nestedRepeats.sql 2012-11-13 11:22 1.9K
nestedRepeats.txt.gz 2012-11-13 11:22 12M
netMm10.sql 2012-11-13 11:22 2.1K
netMm10.txt.gz 2012-11-13 11:22 66M
netMm39.sql 2020-11-26 01:23 2.1K
netMm39.txt.gz 2020-11-26 01:23 66M
rmsk.sql 2012-11-13 11:20 1.9K
rmsk.txt.gz 2012-11-13 11:21 111M
seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:29 642K
simpleRepeat.sql 2012-11-13 11:21 1.9K
simpleRepeat.txt.gz 2012-11-13 11:21 15M
tableDescriptions.sql 2024-11-16 02:03 1.5K
tableDescriptions.txt.gz 2024-11-16 02:03 6.3K
tableList.sql 2024-11-17 03:41 1.6K
tableList.txt.gz 2024-11-17 03:41 3.2K
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 47K
ucscToINSDC.sql 2013-09-15 19:27 1.4K
ucscToINSDC.txt.gz 2013-09-15 19:27 89K
ucscToRefSeq.sql 2018-02-18 08:40 1.4K
ucscToRefSeq.txt.gz 2018-02-18 08:40 92K
windowmaskerSdust.sql 2012-11-13 11:22 1.5K
windowmaskerSdust.txt.gz 2012-11-13 11:22 128M
xenoRefFlat.sql 2020-08-20 11:25 1.7K
xenoRefFlat.txt.gz 2020-08-20 11:25 35M
xenoRefGene.sql 2020-08-20 11:21 2.0K
xenoRefGene.txt.gz 2020-08-20 11:21 39M
xenoRefSeqAli.sql 2020-08-20 11:25 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 11:25 41M