This directory contains a dump of the UCSC genome annotation database for the
    Aug. 2012 (allMis0.2/allMis1) assembly of the american alligator genome
    (allMis1, International Crocodilian Genomes Working Group) .

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/13409
    http://www.ncbi.nlm.nih.gov/genome/assembly/406428
    http://www.ncbi.nlm.nih.gov/bioproject/159843

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=allMis1
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/allMis1/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/allMis1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/allMis1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/allMis1/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/allMis1/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 allMis1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql allMis1 --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 - all_est.sql 2016-06-26 05:59 2.1K all_est.txt.gz 2016-06-26 05:59 222K all_mrna.sql 2020-05-05 17:11 2.1K all_mrna.txt.gz 2020-05-05 17:11 11K augustusGene.sql 2015-07-26 09:51 1.9K augustusGene.txt.gz 2015-07-26 09:51 1.8M bigFiles.sql 2021-05-16 03:10 1.4K bigFiles.txt.gz 2021-05-16 03:10 68 chainGalGal6.sql 2019-01-20 07:52 1.7K chainGalGal6.txt.gz 2019-01-20 07:52 23M chainGalGal6Link.sql 2019-01-20 07:52 1.5K chainGalGal6Link.txt.gz 2019-01-20 07:53 276M chainHg19.sql 2013-09-25 15:23 1.7K chainHg19.txt.gz 2013-09-25 15:23 23M chainHg19Link.sql 2013-09-25 15:24 1.5K chainHg19Link.txt.gz 2013-09-25 15:24 302M chromAlias.sql 2018-02-18 05:00 1.4K chromAlias.txt.gz 2018-02-18 05:00 145K chromInfo.sql 2013-09-25 15:25 1.4K chromInfo.txt.gz 2013-09-25 15:25 92K cpgIslandExt.sql 2013-09-25 15:26 1.7K cpgIslandExt.txt.gz 2013-09-25 15:26 530K cpgIslandExtUnmasked.sql 2014-06-01 07:52 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 07:52 781K cytoBandIdeo.sql 2013-09-25 15:26 1.5K cytoBandIdeo.txt.gz 2013-09-25 15:26 86K estOrientInfo.sql 2016-06-26 06:02 1.8K estOrientInfo.txt.gz 2016-06-26 06:02 69K gap.sql 2013-09-25 15:26 1.6K gap.txt.gz 2013-09-25 15:26 1.2M gbLoaded.sql 2020-08-18 01:45 1.6K gbLoaded.txt.gz 2020-08-18 01:45 75K gc5BaseBw.sql 2013-09-25 15:28 1.3K gc5BaseBw.txt.gz 2013-09-25 15:28 63 genscan.sql 2013-09-25 15:26 1.7K genscan.txt.gz 2013-09-25 15:26 2.6M gold.sql 2013-09-25 15:26 1.7K gold.txt.gz 2013-09-25 15:26 1.7M grp.sql 2014-03-02 03:37 1.3K grp.txt.gz 2014-03-02 03:37 208 hgFindSpec.sql 2021-01-21 09:35 1.8K hgFindSpec.txt.gz 2021-01-21 09:35 609 history.sql 2013-09-25 15:26 1.6K history.txt.gz 2013-09-25 15:26 455 intronEst.sql 2016-06-26 05:59 2.1K intronEst.txt.gz 2016-06-26 05:59 120K microsat.sql 2015-08-23 09:21 1.5K microsat.txt.gz 2015-08-23 09:21 180K mrnaOrientInfo.sql 2020-05-05 17:11 1.8K mrnaOrientInfo.txt.gz 2020-05-05 17:11 3.1K nestedRepeats.sql 2013-09-25 15:23 1.9K nestedRepeats.txt.gz 2013-09-25 15:23 5.8M netGalGal6.sql 2019-01-20 07:54 2.1K netGalGal6.txt.gz 2019-01-20 07:54 40M netHg19.sql 2013-09-25 15:25 2.1K netHg19.txt.gz 2013-09-25 15:25 15M refFlat.sql 2020-08-18 01:13 1.7K refFlat.txt.gz 2020-08-18 01:13 3.8K refGene.sql 2020-08-18 01:13 1.9K refGene.txt.gz 2020-08-18 01:13 4.2K refSeqAli.sql 2019-10-20 06:29 2.1K refSeqAli.txt.gz 2019-10-20 06:29 4.8K rmsk.sql 2013-09-25 15:28 1.9K rmsk.txt.gz 2013-09-25 15:28 78M simpleRepeat.sql 2013-09-25 15:28 1.9K simpleRepeat.txt.gz 2013-09-25 15:28 9.4M tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 5.1K tableList.sql 2021-05-16 03:10 1.6K tableList.txt.gz 2021-05-16 03:10 2.7K trackDb.sql 2021-01-21 09:35 2.1K trackDb.txt.gz 2021-01-21 09:35 40K ucscToRefSeq.sql 2018-02-18 05:00 1.4K ucscToRefSeq.txt.gz 2018-02-18 05:00 126K windowmaskerSdust.sql 2013-09-25 15:28 1.5K windowmaskerSdust.txt.gz 2013-09-25 15:28 111M xenoMrna.sql 2020-08-18 01:13 2.1K xenoMrna.txt.gz 2020-08-18 01:13 256M xenoRefFlat.sql 2020-08-18 01:43 1.7K xenoRefFlat.txt.gz 2020-08-18 01:43 27M xenoRefGene.sql 2020-08-18 01:30 1.9K xenoRefGene.txt.gz 2020-08-18 01:30 30M xenoRefSeqAli.sql 2020-08-18 01:43 2.1K xenoRefSeqAli.txt.gz 2020-08-18 01:43 29M