This directory contains a dump of the UCSC genome annotation database for the
    Jun 2013 (Macaca_fascicularis_5.0/macFas5) assembly of the crab-eating macaque genome
    (macFas5, Washington University (WashU) GCA_000364345.1) .

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/776
    http://www.ncbi.nlm.nih.gov/genome/assembly/704988
    http://www.ncbi.nlm.nih.gov/bioproject/215851

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=macFas5
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/macFas5/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/macFas5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/macFas5/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.soe.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 macFas5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql macFas5 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

The Crab-eating macaque sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, 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 these data
   if the providers of these data are properly acknowledged.  See
   http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. The centers producing the data reserve 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.

-----------------------------------------------------------------------------
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 2016-04-07 12:44 2.1K all_est.txt.gz 2016-04-07 12:44 9.7M augustusGene.sql 2016-04-07 12:44 1.9K gold.sql 2016-04-07 12:44 1.7K gold.txt.gz 2016-04-07 12:44 1.5M grp.sql 2016-04-07 12:44 1.3K grp.txt.gz 2016-04-07 12:44 206 augustusGene.txt.gz 2016-04-07 12:44 2.2M chainHg19.sql 2016-04-07 12:44 1.7K history.sql 2016-04-07 12:44 1.6K history.txt.gz 2016-04-07 12:44 887 chainHg19.txt.gz 2016-04-07 12:44 15M intronEst.sql 2016-04-07 12:44 2.1K intronEst.txt.gz 2016-04-07 12:44 7.1M chainHg19Link.sql 2016-04-07 12:44 1.5K chainHg19Link.txt.gz 2016-04-07 12:45 177M chainHg38.sql 2016-04-07 12:45 1.7K chainHg38.txt.gz 2016-04-07 12:46 256M chainHg38Link.sql 2016-04-07 12:47 1.5K chainHg38Link.txt.gz 2016-04-07 12:48 783M chainPapHam1.sql 2016-04-07 12:51 1.7K chainPapHam1.txt.gz 2016-04-07 12:51 24M chainPapHam1Link.sql 2016-04-07 12:51 1.5K chainPapHam1Link.txt.gz 2016-04-07 12:51 84M chainTarSyr2.sql 2016-04-07 12:51 1.7K chainTarSyr2.txt.gz 2016-04-07 12:52 291M chainTarSyr2Link.sql 2016-04-07 12:53 1.5K chainTarSyr2Link.txt.gz 2016-04-07 12:54 1.2G chromInfo.sql 2016-04-07 12:59 1.4K chromInfo.txt.gz 2016-04-07 12:59 40K cpgIslandExt.sql 2016-04-07 12:59 1.7K cpgIslandExt.txt.gz 2016-04-07 12:59 607K cpgIslandExtUnmasked.sql 2016-04-07 12:59 1.7K cpgIslandExtUnmasked.txt.gz 2016-04-07 12:59 1.5M cytoBandIdeo.sql 2016-04-07 12:59 1.5K cytoBandIdeo.txt.gz 2016-04-07 12:59 38K gc5BaseBw.sql 2016-04-07 12:59 1.3K gc5BaseBw.txt.gz 2016-04-07 12:59 63 estOrientInfo.sql 2016-04-07 12:59 1.8K estOrientInfo.txt.gz 2016-04-07 12:59 1.8M genscan.sql 2016-04-07 12:59 1.7K genscan.txt.gz 2016-04-07 12:59 2.9M gap.sql 2016-04-07 12:59 1.6K gap.txt.gz 2016-04-07 12:59 1.1M microsat.sql 2016-04-07 12:59 1.5K microsat.txt.gz 2016-04-07 12:59 373K netHg19.sql 2016-04-07 12:59 2.1K netHg19.txt.gz 2016-04-07 12:59 21M netHg38.sql 2016-04-07 12:59 2.1K netHg38.txt.gz 2016-04-07 12:59 22M windowmaskerSdust.sql 2016-04-07 12:59 1.5K windowmaskerSdust.txt.gz 2016-04-07 12:59 104M netPapHam1.sql 2016-04-07 12:59 2.1K netPapHam1.txt.gz 2016-04-07 12:59 19M netTarSyr2.sql 2016-04-07 13:00 2.1K netTarSyr2.txt.gz 2016-04-07 13:00 67M rmsk.sql 2016-04-07 13:00 1.9K rmsk.txt.gz 2016-04-07 13:00 135M simpleRepeat.sql 2016-04-07 13:01 1.9K simpleRepeat.txt.gz 2016-04-07 13:01 25M chromAlias.sql 2018-02-04 08:05 1.4K chromAlias.txt.gz 2018-02-04 08:05 82K ucscToINSDC.sql 2018-02-04 08:05 1.4K ucscToINSDC.txt.gz 2018-02-04 08:05 57K ucscToRefSeq.sql 2018-02-04 08:05 1.4K ucscToRefSeq.txt.gz 2018-02-04 08:05 60K refSeqAli.sql 2020-03-01 07:36 2.1K refSeqAli.txt.gz 2020-03-01 07:36 207K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 ncbiRefSeq.sql 2020-05-10 03:28 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:28 3.7M ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 435K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 165K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:28 2.0M ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 10M ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.6M ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 5.3M seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 1.1M all_mrna.sql 2020-08-19 14:23 2.1K mrnaOrientInfo.sql 2020-08-19 14:23 1.8K all_mrna.txt.gz 2020-08-19 14:23 1.0M mrnaOrientInfo.txt.gz 2020-08-19 14:23 258K refGene.sql 2020-08-19 14:37 1.9K refGene.txt.gz 2020-08-19 14:37 200K refFlat.sql 2020-08-19 14:40 1.7K refFlat.txt.gz 2020-08-19 14:40 187K xenoRefFlat.sql 2020-08-19 14:40 1.7K xenoRefGene.sql 2020-08-19 14:40 1.9K xenoRefSeqAli.sql 2020-08-19 14:40 2.1K xenoRefGene.txt.gz 2020-08-19 14:40 33M xenoRefFlat.txt.gz 2020-08-19 14:40 30M xenoRefSeqAli.txt.gz 2020-08-19 14:40 32M gbLoaded.sql 2020-08-19 14:53 1.6K gbLoaded.txt.gz 2020-08-19 14:53 44K ensGene.sql 2020-08-31 15:39 1.9K ensGene.txt.gz 2020-08-31 15:39 3.2M ensGtp.sql 2020-08-31 15:39 1.4K ensemblToGeneName.sql 2020-08-31 15:39 1.4K ensGtp.txt.gz 2020-08-31 15:39 486K ensemblToGeneName.txt.gz 2020-08-31 15:39 249K ensemblSource.sql 2020-08-31 16:00 1.4K ensemblSource.txt.gz 2020-08-31 16:00 145K ensPep.sql 2020-08-31 16:00 1.3K ensPep.txt.gz 2020-08-31 16:00 7.4M chainCalJac4.sql 2020-11-03 01:39 1.7K chainCalJac4.txt.gz 2020-11-03 01:39 435M chainCalJac4Link.sql 2020-11-03 01:51 1.6K chainCalJac4Link.txt.gz 2020-11-03 01:51 1.3G netCalJac4.sql 2020-11-03 01:54 2.1K netCalJac4.txt.gz 2020-11-03 01:54 49M tableDescriptions.sql 2021-07-30 06:33 1.4K tableDescriptions.txt.gz 2021-07-30 06:33 7.6K trackDb_pushedout.sql 2022-04-26 10:29 2.1K trackDb_pushedout.txt.gz 2022-04-26 10:29 50K hgFindSpec_pushedout.sql 2022-04-26 10:29 1.8K hgFindSpec_pushedout.txt.gz 2022-04-26 10:29 1.2K trackDb.sql 2022-05-06 12:33 2.1K trackDb.txt.gz 2022-05-06 12:33 49K hgFindSpec.sql 2022-05-06 12:33 1.8K hgFindSpec.txt.gz 2022-05-06 12:33 1.2K tableList.sql 2022-08-14 03:11 1.6K tableList.txt.gz 2022-08-14 03:11 3.9K bigFiles.sql 2022-08-14 03:11 1.4K bigFiles.txt.gz 2022-08-14 03:11 94