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 -
rmsk.sql 2018-09-28 12:50 1.9K
rmsk.txt.gz 2018-09-28 12:50 18M
all_mrna.sql 2018-09-28 12:50 2.1K
all_mrna.txt.gz 2018-09-28 12:50 3.8K
microsat.sql 2018-09-28 12:50 1.5K
microsat.txt.gz 2018-09-28 12:50 325K
augustusGene.sql 2018-09-28 12:50 1.9K
augustusGene.txt.gz 2018-09-28 12:50 1.5M
chainHg38.sql 2018-09-28 12:50 1.7K
chainHg38.txt.gz 2018-09-28 12:50 62M
chainHg38Link.sql 2018-09-28 12:50 1.5K
mrnaOrientInfo.sql 2018-09-28 12:50 1.8K
mrnaOrientInfo.txt.gz 2018-09-28 12:50 945
chainHg38Link.txt.gz 2018-09-28 12:51 251M
simpleRepeat.sql 2018-09-28 12:52 1.9K
simpleRepeat.txt.gz 2018-09-28 12:52 14M
chainMm10.sql 2018-09-28 12:52 1.7K
chainMm10.txt.gz 2018-09-28 12:52 18M
chainMm10Link.sql 2018-09-28 12:52 1.5K
chainMm10Link.txt.gz 2018-09-28 12:52 143M
chromAlias.sql 2018-09-28 12:53 1.4K
chromAlias.txt.gz 2018-09-28 12:53 79K
chromInfo.sql 2018-09-28 12:53 1.4K
chromInfo.txt.gz 2018-09-28 12:53 43K
cpgIslandExt.sql 2018-09-28 12:53 1.7K
cpgIslandExt.txt.gz 2018-09-28 12:53 400K
cpgIslandExtUnmasked.sql 2018-09-28 12:53 1.7K
cpgIslandExtUnmasked.txt.gz 2018-09-28 12:53 756K
history.sql 2018-09-28 12:53 1.6K
history.txt.gz 2018-09-28 12:53 858
cytoBandIdeo.sql 2018-09-28 12:53 1.5K
cytoBandIdeo.txt.gz 2018-09-28 12:53 41K
gap.sql 2018-09-28 12:53 1.6K
gap.txt.gz 2018-09-28 12:53 2.1M
gc5BaseBw.sql 2018-09-28 12:53 1.3K
gc5BaseBw.txt.gz 2018-09-28 12:53 66
genscan.sql 2018-09-28 12:53 1.7K
genscan.txt.gz 2018-09-28 12:53 1.3M
ucscToINSDC.sql 2018-09-28 12:53 1.4K
ucscToINSDC.txt.gz 2018-09-28 12:53 59K
ucscToRefSeq.sql 2018-09-28 12:53 1.4K
ucscToRefSeq.txt.gz 2018-09-28 12:53 57K
windowmaskerSdust.sql 2018-09-28 12:53 1.5K
windowmaskerSdust.txt.gz 2018-09-28 12:53 66M
gold.sql 2018-09-28 12:53 1.7K
gold.txt.gz 2018-09-28 12:53 2.8M
xenoRefFlat.sql 2018-09-28 12:53 1.7K
xenoRefFlat.txt.gz 2018-09-28 12:53 22M
grp.sql 2018-09-28 12:53 1.3K
grp.txt.gz 2018-09-28 12:53 213
nestedRepeats.sql 2018-09-28 12:53 1.9K
nestedRepeats.txt.gz 2018-09-28 12:53 571K
netHg38.sql 2018-09-28 12:53 2.1K
netHg38.txt.gz 2018-09-28 12:53 7.3M
netMm10.sql 2018-09-28 12:53 2.1K
netMm10.txt.gz 2018-09-28 12:53 6.5M
xenoRefGene.sql 2018-09-28 12:53 1.9K
xenoRefGene.txt.gz 2018-09-28 12:53 24M
xenoRefSeqAli.sql 2018-09-28 12:53 2.1K
xenoRefSeqAli.txt.gz 2018-09-28 12:53 20M
chainGalGal6.sql 2019-01-20 20:24 1.7K
chainGalGal6.txt.gz 2019-01-20 20:24 15M
netGalGal6.sql 2019-01-20 20:24 2.1K
netGalGal6.txt.gz 2019-01-20 20:24 11M
chainGalGal6Link.sql 2019-01-20 20:24 1.5K
chainGalGal6Link.txt.gz 2019-01-20 20:25 85M
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 5.4M
seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:29 410K
ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 1.7M
ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 2.0M
extNcbiRefSeq.sql 2020-05-10 03:29 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:29 90
ncbiRefSeq.sql 2020-05-10 03:29 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:29 1.7M
ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:29 164K
ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:29 863K
trackDb.sql 2023-12-05 13:52 2.1K
trackDb.txt.gz 2023-12-05 13:52 29K
hgFindSpec.sql 2023-12-05 13:52 1.8K
hgFindSpec.txt.gz 2023-12-05 13:52 939
tableDescriptions.sql 2024-11-23 02:04 1.5K
tableDescriptions.txt.gz 2024-11-23 02:04 6.0K
tableList.sql 2024-11-24 03:05 1.6K
tableList.txt.gz 2024-11-24 03:05 2.9K
bigFiles.sql 2024-11-24 03:05 1.4K
bigFiles.txt.gz 2024-11-24 03:05 95