This directory contains a dump of the UCSC genome annotation database for
the Sep. 2010 (WUGSC 7.0/petMar2) assembly of the lamprey genome (petMar2, GSC Washington University School of Medicine).
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/287
http://www.ncbi.nlm.nih.gov/genome/assembly/171978
http://www.ncbi.nlm.nih.gov/bioproject/12880
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=petMar2
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/petMar2/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/petMar2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/petMar2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/petMar2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/petMar2/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 petMar2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql petMar2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Lamprey 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.
-----------------------------------------------------------------------------
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 -
phastConsElements7way.sql 2013-01-07 16:05 1.6K
gold.sql 2013-01-07 16:05 1.7K
gold.txt.gz 2013-01-07 16:05 1.0M
phastConsElements7way.txt.gz 2013-01-07 16:05 2.1M
chainMm10.sql 2013-01-07 16:05 1.7K
chainMm10.txt.gz 2013-01-07 16:05 8.3M
chainBraFlo2Link.sql 2013-01-07 16:05 1.6K
chainBraFlo2Link.txt.gz 2013-01-07 16:05 22M
chainOryLat2Link.sql 2013-01-07 16:05 1.6K
chainOryLat2Link.txt.gz 2013-01-07 16:05 102M
all_est.sql 2013-01-07 16:05 2.1K
all_est.txt.gz 2013-01-07 16:05 4.2M
chainHg19Link.sql 2013-01-07 16:05 1.5K
chainHg19Link.txt.gz 2013-01-07 16:05 39M
chainGalGal4.sql 2013-01-07 16:06 1.7K
chainGalGal4.txt.gz 2013-01-07 16:06 2.7M
windowmaskerSdust.sql 2013-01-07 16:06 1.5K
windowmaskerSdust.txt.gz 2013-01-07 16:06 30M
multiz7way.sql 2013-01-07 16:06 1.5K
multiz7way.txt.gz 2013-01-07 16:06 9.2M
chainGalGal4Link.sql 2013-01-07 16:06 1.6K
multiz7waySummary.sql 2013-01-07 16:06 1.6K
multiz7waySummary.txt.gz 2013-01-07 16:06 137K
chainGalGal4Link.txt.gz 2013-01-07 16:06 12M
netOryLat2.sql 2013-01-07 16:06 2.1K
netOryLat2.txt.gz 2013-01-07 16:06 3.4M
chainHg19.sql 2013-01-07 16:06 1.7K
chainHg19.txt.gz 2013-01-07 16:06 11M
extFile.sql 2013-01-07 16:06 1.4K
extFile.txt.gz 2013-01-07 16:06 78
gap.sql 2013-01-07 16:06 1.6K
gap.txt.gz 2013-01-07 16:06 532K
multiz7wayFrames.sql 2013-01-07 16:06 1.7K
multiz7wayFrames.txt.gz 2013-01-07 16:06 6.7M
gc5BaseBw.sql 2013-01-07 16:06 1.3K
gc5BaseBw.txt.gz 2013-01-07 16:06 63
netBraFlo2.sql 2013-01-07 16:06 2.1K
chainMonDom5.sql 2013-01-07 16:06 1.7K
netBraFlo2.txt.gz 2013-01-07 16:06 2.0M
chainMonDom5.txt.gz 2013-01-07 16:06 13M
chainMm10Link.sql 2013-01-07 16:06 1.5K
chainMm10Link.txt.gz 2013-01-07 16:06 26M
netHg19.sql 2013-01-07 16:06 2.1K
netHg19.txt.gz 2013-01-07 16:06 2.6M
simpleRepeat.sql 2013-01-07 16:06 1.9K
simpleRepeat.txt.gz 2013-01-07 16:06 10M
cpgIslandExt.sql 2013-01-07 16:06 1.7K
cpgIslandExt.txt.gz 2013-01-07 16:06 1.6M
netGalGal4.sql 2013-01-07 16:06 2.1K
netGalGal4.txt.gz 2013-01-07 16:06 2.4M
phastCons7way.sql 2013-01-07 16:07 1.8K
phastCons7way.txt.gz 2013-01-07 16:07 3.7M
genscan.sql 2013-01-07 16:07 1.7K
genscan.txt.gz 2013-01-07 16:07 1.2M
history.sql 2013-01-07 16:07 1.6K
history.txt.gz 2013-01-07 16:07 842
genscanSubopt.sql 2013-01-07 16:07 1.6K
genscanSubopt.txt.gz 2013-01-07 16:07 2.2M
chainBraFlo2.sql 2013-01-07 16:07 1.7K
chromInfo.sql 2013-01-07 16:07 1.4K
chromInfo.txt.gz 2013-01-07 16:07 129K
chainBraFlo2.txt.gz 2013-01-07 16:07 4.2M
netMm10.sql 2013-01-07 16:07 2.1K
netMm10.txt.gz 2013-01-07 16:07 2.6M
netMonDom5.sql 2013-01-07 16:07 2.1K
estOrientInfo.sql 2013-01-07 16:07 1.8K
estOrientInfo.txt.gz 2013-01-07 16:07 1.1M
netMonDom5.txt.gz 2013-01-07 16:07 2.2M
phyloP7way.sql 2013-01-07 16:07 1.8K
phyloP7way.txt.gz 2013-01-07 16:07 3.8M
rmsk.sql 2013-01-07 16:07 1.9K
rmsk.txt.gz 2013-01-07 16:07 11M
chainMonDom5Link.sql 2013-01-07 16:07 1.6K
chainMonDom5Link.txt.gz 2013-01-07 16:07 41M
intronEst.sql 2013-01-07 16:07 2.1K
intronEst.txt.gz 2013-01-07 16:07 1.5M
nestedRepeats.sql 2013-01-07 16:07 1.9K
nestedRepeats.txt.gz 2013-01-07 16:07 936K
chainOryLat2.sql 2013-01-07 16:07 1.7K
chainOryLat2.txt.gz 2013-01-07 16:07 20M
cytoBandIdeo.sql 2013-04-28 20:51 1.5K
cytoBandIdeo.txt.gz 2013-04-28 20:51 119K
ucscToINSDC.sql 2013-09-15 18:29 1.4K
ucscToINSDC.txt.gz 2013-09-15 18:29 178K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 18:51 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:51 2.6M
lampreyGene.sql 2014-06-15 18:49 1.7K
lampreyGene.txt.gz 2014-06-15 18:49 1.1M
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 1.7M
microsat.sql 2015-08-24 00:20 1.5K
microsat.txt.gz 2015-08-24 00:20 99
chromAlias.sql 2018-08-05 08:57 1.4K
chromAlias.txt.gz 2018-08-05 08:57 118K
all_mrna.sql 2020-08-22 22:18 2.1K
all_mrna.txt.gz 2020-08-22 22:18 115K
mrnaOrientInfo.sql 2020-08-22 22:18 1.8K
mrnaOrientInfo.txt.gz 2020-08-22 22:18 27K
xenoRefGene.sql 2020-08-22 22:18 2.0K
xenoRefGene.txt.gz 2020-08-22 22:18 8.2M
xenoRefFlat.sql 2020-08-22 22:18 1.7K
xenoRefFlat.txt.gz 2020-08-22 22:18 7.5M
xenoRefSeqAli.sql 2020-08-22 22:18 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 22:18 8.0M
gbLoaded.sql 2020-08-22 22:18 1.6K
gbLoaded.txt.gz 2020-08-22 22:18 82K
ensGene.sql 2021-05-25 14:43 1.9K
ensGene.txt.gz 2021-05-25 14:43 947K
ensGtp.sql 2021-05-25 14:43 1.4K
ensGtp.txt.gz 2021-05-25 14:43 130K
ensemblToGeneName.sql 2021-05-25 14:43 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:43 42K
ensemblSource.sql 2021-05-25 14:44 1.4K
ensemblSource.txt.gz 2021-05-25 14:44 36K
ensPep.sql 2021-05-25 14:44 1.3K
ensPep.txt.gz 2021-05-25 14:44 2.4M
trackDb.sql 2023-03-28 13:52 2.1K
trackDb.txt.gz 2023-03-28 13:52 44K
hgFindSpec.sql 2023-03-28 13:52 1.8K
hgFindSpec.txt.gz 2023-03-28 13:52 844
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 6.6K
tableList.sql 2024-11-17 03:16 1.6K
tableList.txt.gz 2024-11-17 03:16 3.6K
bigFiles.sql 2024-11-17 03:16 1.4K
bigFiles.txt.gz 2024-11-17 03:16 68