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.
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Name Last modified Size Description
Parent Directory -
gc5BaseBw.txt.gz 2012-11-13 11:20 63
ncbiRefSeqOther.txt.gz 2020-05-10 03:29 75
extNcbiRefSeq.txt.gz 2020-05-10 03:29 91
bigFiles.txt.gz 2024-04-21 03:37 94
grp.txt.gz 2014-03-02 04:14 208
history.txt.gz 2012-11-13 11:22 560
hgFindSpec.txt.gz 2024-01-31 15:13 1.2K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.2K
gc5BaseBw.sql 2012-11-13 11:20 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:29 1.3K
mrnaOrientInfo.txt.gz 2020-08-20 11:08 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K
ensPep.sql 2021-05-25 14:50 1.3K
grp.sql 2014-03-02 04:14 1.3K
ncbiRefSeqPepTable.sql 2020-05-10 03:29 1.4K
ensemblSource.sql 2021-05-25 14:50 1.4K
chromInfo.sql 2012-11-13 11:22 1.4K
bigFiles.sql 2024-04-21 03:37 1.4K
ensemblToGeneName.sql 2021-05-25 14:48 1.4K
chromAlias.sql 2018-02-18 08:40 1.4K
ucscToINSDC.sql 2013-09-15 19:27 1.4K
ucscToRefSeq.sql 2018-02-18 08:40 1.4K
extNcbiRefSeq.sql 2020-05-10 03:29 1.4K
ensGtp.sql 2021-05-25 14:48 1.4K
tableDescriptions.sql 2024-04-20 02:04 1.5K
microsat.sql 2015-08-24 01:44 1.5K
windowmaskerSdust.sql 2012-11-13 11:22 1.5K
cytoBandIdeo.sql 2013-04-28 21:49 1.5K
chainMm10Link.sql 2012-11-13 11:17 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K
chainMm39Link.sql 2020-11-26 01:20 1.6K
history.sql 2012-11-13 11:22 1.6K
tableList.sql 2024-04-21 03:37 1.6K
gap.sql 2012-11-13 11:23 1.6K
gbLoaded.sql 2020-08-20 11:38 1.6K
gold.sql 2012-11-13 11:22 1.7K
genscan.sql 2012-11-13 11:22 1.7K
cpgIslandExt.sql 2012-11-13 11:22 1.7K
chainMm10.sql 2012-11-13 11:21 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 19:49 1.7K
chainMm39.sql 2020-11-26 01:15 1.7K
xenoRefFlat.sql 2020-08-20 11:25 1.7K
hgFindSpec.sql 2024-01-31 15:13 1.8K
estOrientInfo.sql 2012-11-13 11:22 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K
mrnaOrientInfo.sql 2020-08-20 11:08 1.8K
rmsk.sql 2012-11-13 11:20 1.9K
simpleRepeat.sql 2012-11-13 11:21 1.9K
ncbiRefSeq.sql 2020-05-10 03:29 1.9K
nestedRepeats.sql 2012-11-13 11:22 1.9K
augustusGene.sql 2015-07-26 17:28 1.9K
ensGene.sql 2021-05-25 14:48 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:29 2.0K
xenoRefGene.sql 2020-08-20 11:21 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K
trackDb.sql 2024-01-31 15:13 2.1K
trackDb_pushedout.sql 2023-12-05 13:51 2.1K
netMm10.sql 2012-11-13 11:22 2.1K
all_est.sql 2012-11-13 11:20 2.1K
netMm39.sql 2020-11-26 01:23 2.1K
intronEst.sql 2012-11-13 11:22 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K
all_mrna.sql 2020-08-20 11:08 2.1K
xenoRefSeqAli.sql 2020-08-20 11:25 2.1K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:29 3.2K
tableList.txt.gz 2024-04-21 03:37 3.3K
all_mrna.txt.gz 2020-08-20 11:08 5.2K
tableDescriptions.txt.gz 2024-04-20 02:04 6.3K
trackDb_pushedout.txt.gz 2023-12-05 13:51 31K
trackDb.txt.gz 2024-01-31 15:13 47K
chromInfo.txt.gz 2012-11-13 11:22 58K
cytoBandIdeo.txt.gz 2013-04-28 21:49 61K
estOrientInfo.txt.gz 2012-11-13 11:22 69K
gbLoaded.txt.gz 2020-08-20 11:38 87K
ucscToINSDC.txt.gz 2013-09-15 19:27 89K
ucscToRefSeq.txt.gz 2018-02-18 08:40 92K
ensemblSource.txt.gz 2021-05-25 14:50 100K
chromAlias.txt.gz 2018-02-18 08:40 113K
intronEst.txt.gz 2012-11-13 11:22 137K
ensemblToGeneName.txt.gz 2021-05-25 14:48 161K
ncbiRefSeqCds.txt.gz 2020-05-10 03:29 260K
all_est.txt.gz 2012-11-13 11:20 263K
ensGtp.txt.gz 2021-05-25 14:48 337K
cpgIslandExt.txt.gz 2012-11-13 11:22 564K
cpgIslandExtUnmasked.txt.gz 2014-06-01 19:49 596K
seqNcbiRefSeq.txt.gz 2020-05-10 03:29 642K
microsat.txt.gz 2015-08-24 01:44 833K
ncbiRefSeqLink.txt.gz 2020-05-10 03:29 1.2M
gap.txt.gz 2012-11-13 11:23 1.8M
augustusGene.txt.gz 2015-07-26 17:28 2.2M
ensGene.txt.gz 2021-05-25 14:48 2.4M
gold.txt.gz 2012-11-13 11:22 2.4M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 2.6M
ncbiRefSeq.txt.gz 2020-05-10 03:29 2.6M
genscan.txt.gz 2012-11-13 11:22 3.0M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 3.3M
ensPep.txt.gz 2021-05-25 14:50 8.5M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:29 9.0M
nestedRepeats.txt.gz 2012-11-13 11:22 12M
simpleRepeat.txt.gz 2012-11-13 11:21 15M
xenoRefFlat.txt.gz 2020-08-20 11:25 35M
xenoRefGene.txt.gz 2020-08-20 11:21 39M
xenoRefSeqAli.txt.gz 2020-08-20 11:25 41M
netMm10.txt.gz 2012-11-13 11:22 66M
netMm39.txt.gz 2020-11-26 01:23 66M
chainMm39.txt.gz 2020-11-26 01:15 72M
chainMm10.txt.gz 2012-11-13 11:21 89M
rmsk.txt.gz 2012-11-13 11:21 111M
windowmaskerSdust.txt.gz 2012-11-13 11:22 128M
chainMm39Link.txt.gz 2020-11-26 01:20 558M
chainMm10Link.txt.gz 2012-11-13 11:18 618M