This directory contains a dump of the UCSC genome annotation database for the
Oct. 2006 (AgamP3/anoGam3) assembly of the A. gambiae genome
(anoGam3, The International Consortium for the Sequencing of Anopheles Genome) .
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/46
https://www.ncbi.nlm.nih.gov/genome/assembly/305108
https://www.ncbi.nlm.nih.gov/bioproject/1438
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=anoGam3
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.soe.ucsc.edu, then go to
the directory goldenPath/anoGam3/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/anoGam3/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/anoGam3/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/anoGam3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/anoGam3/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 anoGam3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql anoGam3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
-----------------------------------------------------------------------------
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 -
bigFiles.txt.gz 2024-12-08 03:05 95
bigFiles.sql 2024-12-08 03:05 1.4K
tableList.txt.gz 2024-12-08 03:05 2.4K
tableList.sql 2024-12-08 03:05 1.6K
tableDescriptions.txt.gz 2024-12-07 02:03 5.3K
tableDescriptions.sql 2024-12-07 02:03 1.5K
hgFindSpec.txt.gz 2024-07-25 09:34 866
hgFindSpec.sql 2024-07-25 09:34 1.8K
trackDb.txt.gz 2024-07-25 09:34 48K
trackDb.sql 2024-07-25 09:34 2.1K
grp.txt.gz 2018-10-03 13:59 213
grp.sql 2018-10-03 13:59 1.3K
xenoRefSeqAli.txt.gz 2018-10-03 13:59 2.8M
xenoRefSeqAli.sql 2018-10-03 13:59 2.1K
xenoRefGene.txt.gz 2018-10-03 13:59 3.2M
gold.txt.gz 2018-10-03 13:59 87K
gold.sql 2018-10-03 13:59 1.7K
xenoRefGene.sql 2018-10-03 13:59 1.9K
xenoRefFlat.txt.gz 2018-10-03 13:59 2.9M
genscan.txt.gz 2018-10-03 13:59 1.2M
genscan.sql 2018-10-03 13:59 1.7K
xenoRefFlat.sql 2018-10-03 13:59 1.7K
gc5BaseBw.txt.gz 2018-10-03 13:59 66
gc5BaseBw.sql 2018-10-03 13:59 1.3K
gap.txt.gz 2018-10-03 13:59 751
gap.sql 2018-10-03 13:59 1.6K
estOrientInfo.txt.gz 2018-10-03 13:59 1.6M
estOrientInfo.sql 2018-10-03 13:59 1.8K
ensemblToGeneName.txt.gz 2018-10-03 13:59 13K
ensemblToGeneName.sql 2018-10-03 13:59 1.4K
rmsk.txt.gz 2018-10-03 13:59 5.7M
rmsk.sql 2018-10-03 13:59 1.9K
netDm6.txt.gz 2018-10-03 13:59 1.6M
netDm6.sql 2018-10-03 13:59 2.1K
ensemblSource.txt.gz 2018-10-03 13:59 42K
ensemblSource.sql 2018-10-03 13:59 1.4K
ensPep.txt.gz 2018-10-03 13:59 4.0M
ensPep.sql 2018-10-03 13:59 1.3K
xenoMrna.txt.gz 2018-10-03 13:58 56M
xenoMrna.sql 2018-10-03 13:58 2.1K
ensGtp.txt.gz 2018-10-03 13:58 114K
ensGtp.sql 2018-10-03 13:58 1.4K
windowmaskerSdust.txt.gz 2018-10-03 13:58 13M
windowmaskerSdust.sql 2018-10-03 13:58 1.5K
ucscToRefSeq.txt.gz 2018-10-03 13:58 60K
ucscToRefSeq.sql 2018-10-03 13:58 1.4K
nestedRepeats.txt.gz 2018-10-03 13:58 286K
nestedRepeats.sql 2018-10-03 13:58 1.9K
mrnaOrientInfo.txt.gz 2018-10-03 13:58 657K
mrnaOrientInfo.sql 2018-10-03 13:58 1.8K
microsat.txt.gz 2018-10-03 13:58 44K
microsat.sql 2018-10-03 13:58 1.5K
ensGene.txt.gz 2018-10-03 13:58 745K
ensGene.sql 2018-10-03 13:58 1.9K
cytoBandIdeo.txt.gz 2018-10-03 13:58 41K
cytoBandIdeo.sql 2018-10-03 13:58 1.5K
crispr10KTargets.txt.gz 2018-10-03 13:58 69
crispr10KTargets.sql 2018-10-03 13:58 1.3K
crispr10KRanges.txt.gz 2018-10-03 13:58 33K
crispr10KRanges.sql 2018-10-03 13:58 1.5K
intronEst.txt.gz 2018-10-03 13:58 3.0M
cpgIslandExtUnmasked.txt.gz 2018-10-03 13:58 511K
cpgIslandExtUnmasked.sql 2018-10-03 13:58 1.7K
cpgIslandExt.txt.gz 2018-10-03 13:58 516K
cpgIslandExt.sql 2018-10-03 13:58 1.7K
ucscToINSDC.txt.gz 2018-10-03 13:58 64K
ucscToINSDC.sql 2018-10-03 13:58 1.4K
intronEst.sql 2018-10-03 13:58 2.1K
history.txt.gz 2018-10-03 13:58 697
history.sql 2018-10-03 13:58 1.6K
chromInfo.txt.gz 2018-10-03 13:58 41K
chromInfo.sql 2018-10-03 13:58 1.4K
chromAlias.txt.gz 2018-10-03 13:58 85K
chromAlias.sql 2018-10-03 13:58 1.4K
chainDm6Link.txt.gz 2018-10-03 13:58 14M
chainDm6Link.sql 2018-10-03 13:58 1.5K
chainDm6.txt.gz 2018-10-03 13:58 2.1M
chainDm6.sql 2018-10-03 13:58 1.7K
augustusGene.txt.gz 2018-10-03 13:58 651K
augustusGene.sql 2018-10-03 13:58 1.9K
all_mrna.txt.gz 2018-10-03 13:58 2.7M
all_mrna.sql 2018-10-03 13:58 2.1K
all_est.txt.gz 2018-10-03 13:58 5.9M
all_est.sql 2018-10-03 13:58 2.1K
simpleRepeat.txt.gz 2018-10-03 13:58 1.9M
simpleRepeat.sql 2018-10-03 13:58 1.9K