This directory contains a dump of the UCSC genome annotation database for the
Jun. 2015 (Thamnophis_sirtalis-6.0/thaSir1) assembly of the garter snake genome
(thaSir1, The Genome Institute at Washington University School of Medicine (WUGSC)) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
https://www.ncbi.nlm.nih.gov/genome/16688
https://www.ncbi.nlm.nih.gov/genome/assembly/472161
https://www.ncbi.nlm.nih.gov/bioproject/189551
Files included in this directory (updated weekly):
- *.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=thaSir1
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.soe.ucsc.edu, then go to
the directory goldenPath/thaSir1/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.soe.ucsc.edu/goldenPath/thaSir1/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/thaSir1/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/thaSir1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/thaSir1/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 thaSir1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql thaSir1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Garter snake sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, 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 these data
if the providers of these data are properly acknowledged. See
http://genome.ucsc.edu/goldenPath/credits.html for credit information.
3. The centers producing the data reserve 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.
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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 -
gc5BaseBw.txt.gz 2018-09-28 12:53 66
ncbiRefSeqOther.txt.gz 2020-05-10 03:29 75
extNcbiRefSeq.txt.gz 2020-05-10 03:29 90
bigFiles.txt.gz 2024-04-21 03:06 95
grp.txt.gz 2018-09-28 12:53 213
history.txt.gz 2018-09-28 12:53 858
hgFindSpec.txt.gz 2023-12-05 13:52 939
mrnaOrientInfo.txt.gz 2018-09-28 12:50 945
hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 949
gc5BaseBw.sql 2018-09-28 12:53 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:29 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K
grp.sql 2018-09-28 12:53 1.3K
ncbiRefSeqPepTable.sql 2020-05-10 03:29 1.4K
chromInfo.sql 2018-09-28 12:53 1.4K
bigFiles.sql 2024-04-21 03:06 1.4K
chromAlias.sql 2018-09-28 12:53 1.4K
ucscToINSDC.sql 2018-09-28 12:53 1.4K
ucscToRefSeq.sql 2018-09-28 12:53 1.4K
extNcbiRefSeq.sql 2020-05-10 03:29 1.4K
tableDescriptions.sql 2024-04-20 02:04 1.5K
microsat.sql 2018-09-28 12:50 1.5K
windowmaskerSdust.sql 2018-09-28 12:53 1.5K
cytoBandIdeo.sql 2018-09-28 12:53 1.5K
chainHg38Link.sql 2018-09-28 12:50 1.5K
chainMm10Link.sql 2018-09-28 12:52 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K
chainGalGal6Link.sql 2019-01-20 20:24 1.5K
history.sql 2018-09-28 12:53 1.6K
tableList.sql 2024-04-21 03:06 1.6K
gap.sql 2018-09-28 12:53 1.6K
gold.sql 2018-09-28 12:53 1.7K
genscan.sql 2018-09-28 12:53 1.7K
cpgIslandExt.sql 2018-09-28 12:53 1.7K
chainHg38.sql 2018-09-28 12:50 1.7K
chainMm10.sql 2018-09-28 12:52 1.7K
chainGalGal6.sql 2019-01-20 20:24 1.7K
cpgIslandExtUnmasked.sql 2018-09-28 12:53 1.7K
xenoRefFlat.sql 2018-09-28 12:53 1.7K
hgFindSpec.sql 2023-12-05 13:52 1.8K
mrnaOrientInfo.sql 2018-09-28 12:50 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K
rmsk.sql 2018-09-28 12:50 1.9K
simpleRepeat.sql 2018-09-28 12:52 1.9K
ncbiRefSeq.sql 2020-05-10 03:29 1.9K
nestedRepeats.sql 2018-09-28 12:53 1.9K
xenoRefGene.sql 2018-09-28 12:53 1.9K
augustusGene.sql 2018-09-28 12:50 1.9K
ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K
trackDb.sql 2023-12-05 13:52 2.1K
trackDb_pushedout.sql 2023-12-05 13:52 2.1K
netHg38.sql 2018-09-28 12:53 2.1K
netMm10.sql 2018-09-28 12:53 2.1K
netGalGal6.sql 2019-01-20 20:24 2.1K
all_mrna.sql 2018-09-28 12:50 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K
xenoRefSeqAli.sql 2018-09-28 12:53 2.1K
tableList.txt.gz 2024-04-21 03:06 3.0K
all_mrna.txt.gz 2018-09-28 12:50 3.8K
tableDescriptions.txt.gz 2024-04-20 02:04 6.0K
trackDb.txt.gz 2023-12-05 13:52 29K
trackDb_pushedout.txt.gz 2023-12-05 13:52 29K
cytoBandIdeo.txt.gz 2018-09-28 12:53 41K
chromInfo.txt.gz 2018-09-28 12:53 43K
ucscToRefSeq.txt.gz 2018-09-28 12:53 57K
ucscToINSDC.txt.gz 2018-09-28 12:53 59K
chromAlias.txt.gz 2018-09-28 12:53 79K
ncbiRefSeqCds.txt.gz 2020-05-10 03:29 164K
microsat.txt.gz 2018-09-28 12:50 325K
cpgIslandExt.txt.gz 2018-09-28 12:53 400K
seqNcbiRefSeq.txt.gz 2020-05-10 03:29 410K
nestedRepeats.txt.gz 2018-09-28 12:53 571K
cpgIslandExtUnmasked.txt.gz 2018-09-28 12:53 756K
ncbiRefSeqLink.txt.gz 2020-05-10 03:29 863K
genscan.txt.gz 2018-09-28 12:53 1.3M
augustusGene.txt.gz 2018-09-28 12:50 1.5M
ncbiRefSeq.txt.gz 2020-05-10 03:29 1.7M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 1.7M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 2.0M
gap.txt.gz 2018-09-28 12:53 2.1M
gold.txt.gz 2018-09-28 12:53 2.8M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:29 5.4M
netMm10.txt.gz 2018-09-28 12:53 6.5M
netHg38.txt.gz 2018-09-28 12:53 7.3M
netGalGal6.txt.gz 2019-01-20 20:24 11M
simpleRepeat.txt.gz 2018-09-28 12:52 14M
chainGalGal6.txt.gz 2019-01-20 20:24 15M
rmsk.txt.gz 2018-09-28 12:50 18M
chainMm10.txt.gz 2018-09-28 12:52 18M
xenoRefSeqAli.txt.gz 2018-09-28 12:53 20M
xenoRefFlat.txt.gz 2018-09-28 12:53 22M
xenoRefGene.txt.gz 2018-09-28 12:53 24M
chainHg38.txt.gz 2018-09-28 12:50 62M
windowmaskerSdust.txt.gz 2018-09-28 12:53 66M
chainGalGal6Link.txt.gz 2019-01-20 20:25 85M
chainMm10Link.txt.gz 2018-09-28 12:52 143M
chainHg38Link.txt.gz 2018-09-28 12:51 251M