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.
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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/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;'
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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 2018-10-03 13:59 66
crispr10KTargets.txt.gz 2018-10-03 13:58 69
bigFiles.txt.gz 2024-12-08 03:05 95
grp.txt.gz 2018-10-03 13:59 213
history.txt.gz 2018-10-03 13:58 697
gap.txt.gz 2018-10-03 13:59 751
hgFindSpec.txt.gz 2024-07-25 09:34 866
gc5BaseBw.sql 2018-10-03 13:59 1.3K
crispr10KTargets.sql 2018-10-03 13:58 1.3K
ensPep.sql 2018-10-03 13:59 1.3K
grp.sql 2018-10-03 13:59 1.3K
ensemblSource.sql 2018-10-03 13:59 1.4K
chromInfo.sql 2018-10-03 13:58 1.4K
ensemblToGeneName.sql 2018-10-03 13:59 1.4K
bigFiles.sql 2024-12-08 03:05 1.4K
ensGtp.sql 2018-10-03 13:58 1.4K
chromAlias.sql 2018-10-03 13:58 1.4K
ucscToINSDC.sql 2018-10-03 13:58 1.4K
ucscToRefSeq.sql 2018-10-03 13:58 1.4K
tableDescriptions.sql 2024-12-07 02:03 1.5K
microsat.sql 2018-10-03 13:58 1.5K
crispr10KRanges.sql 2018-10-03 13:58 1.5K
windowmaskerSdust.sql 2018-10-03 13:58 1.5K
cytoBandIdeo.sql 2018-10-03 13:58 1.5K
chainDm6Link.sql 2018-10-03 13:58 1.5K
history.sql 2018-10-03 13:58 1.6K
tableList.sql 2024-12-08 03:05 1.6K
gap.sql 2018-10-03 13:59 1.6K
gold.sql 2018-10-03 13:59 1.7K
genscan.sql 2018-10-03 13:59 1.7K
cpgIslandExt.sql 2018-10-03 13:58 1.7K
chainDm6.sql 2018-10-03 13:58 1.7K
cpgIslandExtUnmasked.sql 2018-10-03 13:58 1.7K
xenoRefFlat.sql 2018-10-03 13:59 1.7K
estOrientInfo.sql 2018-10-03 13:59 1.8K
mrnaOrientInfo.sql 2018-10-03 13:58 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
rmsk.sql 2018-10-03 13:59 1.9K
ensGene.sql 2018-10-03 13:58 1.9K
simpleRepeat.sql 2018-10-03 13:58 1.9K
nestedRepeats.sql 2018-10-03 13:58 1.9K
xenoRefGene.sql 2018-10-03 13:59 1.9K
augustusGene.sql 2018-10-03 13:58 1.9K
trackDb.sql 2024-07-25 09:34 2.1K
netDm6.sql 2018-10-03 13:59 2.1K
all_est.sql 2018-10-03 13:58 2.1K
all_mrna.sql 2018-10-03 13:58 2.1K
xenoMrna.sql 2018-10-03 13:58 2.1K
intronEst.sql 2018-10-03 13:58 2.1K
xenoRefSeqAli.sql 2018-10-03 13:59 2.1K
tableList.txt.gz 2024-12-08 03:05 2.4K
tableDescriptions.txt.gz 2024-12-07 02:03 5.3K
ensemblToGeneName.txt.gz 2018-10-03 13:59 13K
crispr10KRanges.txt.gz 2018-10-03 13:58 33K
chromInfo.txt.gz 2018-10-03 13:58 41K
cytoBandIdeo.txt.gz 2018-10-03 13:58 41K
ensemblSource.txt.gz 2018-10-03 13:59 42K
microsat.txt.gz 2018-10-03 13:58 44K
trackDb.txt.gz 2024-07-25 09:34 48K
ucscToRefSeq.txt.gz 2018-10-03 13:58 60K
ucscToINSDC.txt.gz 2018-10-03 13:58 64K
chromAlias.txt.gz 2018-10-03 13:58 85K
gold.txt.gz 2018-10-03 13:59 87K
ensGtp.txt.gz 2018-10-03 13:58 114K
nestedRepeats.txt.gz 2018-10-03 13:58 286K
cpgIslandExtUnmasked.txt.gz 2018-10-03 13:58 511K
cpgIslandExt.txt.gz 2018-10-03 13:58 516K
augustusGene.txt.gz 2018-10-03 13:58 651K
mrnaOrientInfo.txt.gz 2018-10-03 13:58 657K
ensGene.txt.gz 2018-10-03 13:58 745K
genscan.txt.gz 2018-10-03 13:59 1.2M
estOrientInfo.txt.gz 2018-10-03 13:59 1.6M
netDm6.txt.gz 2018-10-03 13:59 1.6M
simpleRepeat.txt.gz 2018-10-03 13:58 1.9M
chainDm6.txt.gz 2018-10-03 13:58 2.1M
all_mrna.txt.gz 2018-10-03 13:58 2.7M
xenoRefSeqAli.txt.gz 2018-10-03 13:59 2.8M
xenoRefFlat.txt.gz 2018-10-03 13:59 2.9M
intronEst.txt.gz 2018-10-03 13:58 3.0M
xenoRefGene.txt.gz 2018-10-03 13:59 3.2M
ensPep.txt.gz 2018-10-03 13:59 4.0M
rmsk.txt.gz 2018-10-03 13:59 5.7M
all_est.txt.gz 2018-10-03 13:58 5.9M
windowmaskerSdust.txt.gz 2018-10-03 13:58 13M
chainDm6Link.txt.gz 2018-10-03 13:58 14M
xenoMrna.txt.gz 2018-10-03 13:58 56M