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.
-----------------------------------------------------------------------------
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 2024-03-24 03:07 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 2023-09-19 16:08 857 hgFindSpec_pushedout.txt.gz 2023-09-19 16:08 867 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 bigFiles.sql 2024-03-24 03:07 1.4K chromInfo.sql 2018-10-03 13:58 1.4K ensemblToGeneName.sql 2018-10-03 13:59 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 tableDescriptions.sql 2024-03-23 02:03 1.4K ucscToRefSeq.sql 2018-10-03 13:58 1.4K 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 tableList.sql 2024-03-24 03:07 1.6K history.sql 2018-10-03 13:58 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 hgFindSpec.sql 2023-09-19 16:08 1.8K estOrientInfo.sql 2018-10-03 13:59 1.8K mrnaOrientInfo.sql 2018-10-03 13:58 1.8K hgFindSpec_pushedout.sql 2023-09-19 16:08 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 2023-09-19 16:08 2.1K netDm6.sql 2018-10-03 13:59 2.1K trackDb_pushedout.sql 2023-09-19 16:08 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 2024-03-24 03:07 2.5K tableDescriptions.txt.gz 2024-03-23 02:03 5.3K ensemblToGeneName.txt.gz 2018-10-03 13:59 13K crispr10KRanges.txt.gz 2018-10-03 13:58 33K trackDb.txt.gz 2023-09-19 16:08 40K trackDb_pushedout.txt.gz 2023-09-19 16:08 40K 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 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