This directory contains a dump of the UCSC genome annotation database for
the Aug. 2011 (LatCha1/latCha1) assembly of the coelacanth genome (latCha1,
Broad LatCha1 (GCA_000225785.1)). 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/3262
    http://www.ncbi.nlm.nih.gov/genome/assembly/303548
    http://www.ncbi.nlm.nih.gov/bioproject/56111

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=latCha1
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.cse.ucsc.edu, then go to 
the directory goldenPath/latCha1/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/latCha1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/latCha1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/latCha1/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/latCha1/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 latCha1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql latCha1 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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The Coelacanth sequence is made freely available before scientific publication 
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 particular 
      genes and regions if the provider of these data (The Broad Institute) is 
      properly acknowledged.
   3. The center producing the data reserves 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. 1. The data may 
      be freely downloaded, used in analyses, and repackaged in databases.

-----------------------------------------------------------------------------
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.
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      Name                        Last modified      Size  Description
Parent Directory - xenoRefSeqAli.txt.gz 2020-08-19 13:31 26M xenoRefSeqAli.sql 2020-08-19 13:31 2.1K xenoRefGene.txt.gz 2020-08-19 13:31 29M xenoRefGene.sql 2020-08-19 13:31 2.0K xenoRefFlat.txt.gz 2020-08-19 13:31 27M xenoRefFlat.sql 2020-08-19 13:31 1.7K xenoMrna.txt.gz 2020-08-19 13:07 227M xenoMrna.sql 2020-08-19 13:07 2.1K windowmaskerSdust.txt.gz 2012-11-06 14:17 132M windowmaskerSdust.sql 2012-11-06 14:17 1.5K ucscToRefSeq.txt.gz 2018-02-18 07:15 169K ucscToRefSeq.sql 2018-02-18 07:15 1.4K ucscToINSDC.txt.gz 2013-09-15 15:42 167K ucscToINSDC.sql 2013-09-15 15:42 1.4K trackDb.txt.gz 2023-12-05 13:50 29K trackDb.sql 2023-12-05 13:50 2.1K tableList.txt.gz 2024-05-26 03:43 2.9K tableList.sql 2024-05-26 03:43 1.6K tableDescriptions.txt.gz 2024-05-25 02:03 6.3K tableDescriptions.sql 2024-05-25 02:03 1.5K simpleRepeat.txt.gz 2012-11-06 14:16 14M simpleRepeat.sql 2012-11-06 14:16 1.9K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 615K seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K rmsk.txt.gz 2012-11-06 14:16 42M rmsk.sql 2012-11-06 14:16 1.9K netMm10.txt.gz 2012-11-06 14:16 7.7M netMm10.sql 2012-11-06 14:16 2.1K netFr3.txt.gz 2012-11-06 14:16 6.6M netFr3.sql 2012-11-06 14:16 2.1K nestedRepeats.txt.gz 2012-11-06 14:16 3.4M nestedRepeats.sql 2012-11-06 14:16 1.9K ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.1M ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.6M ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 7.8M ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75 ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.2M ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 796 ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K ncbiRefSeqCds.txt.gz 2020-05-10 03:27 235K ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K ncbiRefSeq.txt.gz 2020-05-10 03:27 2.6M ncbiRefSeq.sql 2020-05-10 03:27 1.9K mrnaOrientInfo.txt.gz 2016-05-15 10:21 1.3K mrnaOrientInfo.sql 2016-05-15 10:21 1.8K microsat.txt.gz 2015-08-23 20:34 663K microsat.sql 2015-08-23 20:34 1.5K history.txt.gz 2012-11-06 14:17 596 history.sql 2012-11-06 14:17 1.6K hgFindSpec.txt.gz 2023-12-05 13:50 1.2K hgFindSpec.sql 2023-12-05 13:50 1.8K grp.txt.gz 2014-03-02 04:14 208 grp.sql 2014-03-02 04:14 1.3K gold.txt.gz 2012-11-06 14:15 4.5M gold.sql 2012-11-06 14:15 1.7K genscan.txt.gz 2012-11-06 14:17 1.8M genscan.sql 2012-11-06 14:17 1.7K gc5BaseBw.txt.gz 2012-11-06 14:15 63 gc5BaseBw.sql 2012-11-06 14:15 1.3K gbLoaded.txt.gz 2020-08-19 13:31 15K gbLoaded.sql 2020-08-19 13:31 1.6K gap.txt.gz 2012-11-06 14:16 3.4M gap.sql 2012-11-06 14:16 1.6K extNcbiRefSeq.txt.gz 2020-05-10 03:27 91 extNcbiRefSeq.sql 2020-05-10 03:27 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:34 131K ensemblToGeneName.sql 2021-05-25 14:34 1.4K ensemblSource.txt.gz 2021-05-25 14:36 71K ensemblSource.sql 2021-05-25 14:36 1.4K ensPep.txt.gz 2021-05-25 14:36 6.4M ensPep.sql 2021-05-25 14:36 1.3K ensGtp.txt.gz 2021-05-25 14:34 255K ensGtp.sql 2021-05-25 14:34 1.4K ensGene.txt.gz 2021-05-25 14:34 2.1M ensGene.sql 2021-05-25 14:34 1.9K cytoBandIdeo.txt.gz 2013-04-28 18:02 115K cytoBandIdeo.sql 2013-04-28 18:02 1.5K cpgIslandExtUnmasked.txt.gz 2014-06-01 16:01 872K cpgIslandExtUnmasked.sql 2014-06-01 16:01 1.7K cpgIslandExt.txt.gz 2012-11-06 14:17 182K cpgIslandExt.sql 2012-11-06 14:17 1.7K chromInfo.txt.gz 2012-11-06 14:17 113K chromInfo.sql 2012-11-06 14:17 1.4K chromAlias.txt.gz 2018-02-18 07:15 215K chromAlias.sql 2018-02-18 07:15 1.4K chainMm10Link.txt.gz 2012-11-06 14:12 140M chainMm10Link.sql 2012-11-06 14:12 1.5K chainMm10.txt.gz 2012-11-06 14:16 16M chainMm10.sql 2012-11-06 14:16 1.7K chainFr3Link.txt.gz 2012-11-06 14:19 41M chainFr3Link.sql 2012-11-06 14:19 1.5K chainFr3.txt.gz 2012-11-06 14:16 9.7M chainFr3.sql 2012-11-06 14:16 1.7K bigFiles.txt.gz 2024-05-26 03:43 94 bigFiles.sql 2024-05-26 03:43 1.4K augustusGene.txt.gz 2015-07-26 15:56 1.8M augustusGene.sql 2015-07-26 15:56 1.9K all_mrna.txt.gz 2016-05-15 10:23 5.1K all_mrna.sql 2016-05-15 10:23 2.1K