This directory contains a dump of the UCSC genome annotation database for
the Feb. 2008 assembly of the guinea pig genome (cavPor3, Broad Institute cavPor3).
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the Broad Institute at MIT and Harvard.
For more information on the guinea pig genome, see the project website:
  http://www.broad.mit.edu/mammals/
  
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=cavPor3
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/cavPor3/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/cavPor3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/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 cavPor3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql cavPor3 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

The Guinea Pig 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.

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 06:05 2.1K all_est.txt.gz 2016-06-26 06:05 1.1M all_mrna.sql 2020-05-06 01:22 2.1K all_mrna.txt.gz 2020-05-06 01:22 298K augustusGene.sql 2015-07-26 11:11 1.9K augustusGene.txt.gz 2015-07-26 11:11 2.7M bigFiles.sql 2021-05-02 03:10 1.4K bigFiles.txt.gz 2021-05-02 03:10 73 blastHg18KG.sql 2009-12-20 10:45 2.3K blastHg18KG.txt.gz 2009-12-20 10:45 3.5M chainGalGal3.sql 2008-06-05 11:25 1.7K chainGalGal3.txt.gz 2008-06-05 11:25 27M chainGalGal3Link.sql 2008-06-05 11:25 1.4K chainGalGal3Link.txt.gz 2008-06-05 11:28 191M chainGalVar1.sql 2016-09-18 07:08 1.7K chainGalVar1.txt.gz 2016-09-18 07:09 701M chainGalVar1Link.sql 2016-09-18 07:11 1.5K chainGalVar1Link.txt.gz 2016-09-18 07:14 2.1G chainHg19.sql 2009-09-20 08:28 1.8K chainHg19.txt.gz 2009-09-20 08:30 570M chainHg19Link.sql 2009-09-20 08:12 1.6K chainHg19Link.txt.gz 2009-09-20 08:17 2.1G chainMm10.sql 2013-10-27 10:59 1.7K chainMm10.txt.gz 2013-10-27 10:59 111M chainMm10Link.sql 2013-10-27 10:59 1.5K chainMm10Link.txt.gz 2013-10-27 11:00 706M chainMm39.sql 2020-11-26 02:53 1.7K chainMm39.txt.gz 2020-11-26 02:53 62M chainMm39Link.sql 2020-11-26 02:56 1.6K chainMm39Link.txt.gz 2020-11-26 02:56 506M chainMonDom4.sql 2008-06-05 12:18 1.7K chainMonDom4.txt.gz 2008-06-05 12:22 385M chainMonDom4Link.sql 2008-06-05 12:27 1.5K chainMonDom4Link.txt.gz 2008-06-05 12:49 1.8G chainOryCun2.sql 2010-05-02 11:22 1.6K chainOryCun2.txt.gz 2010-05-02 11:23 518M chainOryCun2Link.sql 2010-05-02 11:25 1.5K chainOryCun2Link.txt.gz 2010-05-02 11:30 2.0G chainRn6.sql 2017-03-26 17:10 1.7K chainRn6.txt.gz 2017-03-26 17:11 81M chainRn6Link.sql 2017-03-26 17:13 1.5K chainRn6Link.txt.gz 2017-03-26 17:21 607M chromAlias.sql 2018-02-18 05:44 1.4K chromAlias.txt.gz 2018-02-18 05:44 29K chromInfo.sql 2008-06-05 13:34 1.2K chromInfo.txt.gz 2008-06-05 13:34 18K cpgIslandExt.sql 2008-06-05 13:34 1.6K cpgIslandExt.txt.gz 2008-06-05 13:34 820K cpgIslandExtUnmasked.sql 2014-06-01 09:51 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 09:51 841K cytoBandIdeo.sql 2013-04-28 11:40 1.5K cytoBandIdeo.txt.gz 2013-04-28 11:40 18K ensGene.sql 2020-08-31 15:21 1.9K ensGene.txt.gz 2020-08-31 15:21 2.4M ensGtp.sql 2020-08-31 15:21 1.4K ensGtp.txt.gz 2020-08-31 15:21 346K ensPep.sql 2020-08-31 15:44 1.3K ensPep.txt.gz 2020-08-31 15:44 8.2M ensemblSource.sql 2020-08-31 15:44 1.4K ensemblSource.txt.gz 2020-08-31 15:44 105K ensemblToGeneName.sql 2020-08-31 15:21 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:21 173K estOrientInfo.sql 2016-06-26 06:05 1.8K estOrientInfo.txt.gz 2016-06-26 06:05 341K extNcbiRefSeq.sql 2020-05-10 03:26 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:26 91 gap.sql 2008-06-05 13:34 1.5K gap.txt.gz 2008-06-05 13:34 819K gbLoaded.sql 2020-08-18 13:30 1.6K gbLoaded.txt.gz 2020-08-18 13:30 113K gc5Base.sql 2008-06-05 13:36 1.7K gc5Base.txt.gz 2008-06-05 13:36 11M genscan.sql 2008-06-05 13:36 1.6K genscan.txt.gz 2008-06-05 13:36 4.2M genscanPep.sql 2008-06-05 13:36 1.2K genscanPep.txt.gz 2008-06-05 13:36 15M genscanSubopt.sql 2008-06-05 13:36 1.5K genscanSubopt.txt.gz 2008-06-05 13:36 6.4M gold.sql 2008-06-05 13:36 1.6K gold.txt.gz 2008-06-05 13:36 1.1M grp.sql 2014-03-02 03:40 1.4K grp.txt.gz 2014-03-02 03:40 208 hgFindSpec.sql 2021-03-26 09:06 1.8K hgFindSpec.txt.gz 2021-03-26 09:06 1.3K history.sql 2008-06-05 13:36 1.4K history.txt.gz 2008-06-05 13:36 727 intronEst.sql 2016-06-26 06:05 2.1K intronEst.txt.gz 2016-06-26 06:05 534K microsat.sql 2015-08-23 11:56 1.5K microsat.txt.gz 2015-08-23 11:56 748K mrnaOrientInfo.sql 2020-05-06 01:22 1.8K mrnaOrientInfo.txt.gz 2020-05-06 01:22 101K ncbiRefSeq.sql 2020-05-10 03:26 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:26 2.8M ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 255K ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 40K ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.3M ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 9.2M ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.8M ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.3M nestedRepeats.sql 2008-06-05 13:38 1.9K nestedRepeats.txt.gz 2008-06-05 13:39 9.1M netGalGal3.sql 2008-06-05 13:39 2.2K netGalGal3.txt.gz 2008-06-05 13:39 13M netGalVar1.sql 2016-09-18 07:23 2.1K netGalVar1.txt.gz 2016-09-18 07:23 65M netHg19.sql 2009-09-20 08:12 2.3K netHg19.txt.gz 2009-09-20 08:12 57M netMm10.sql 2013-10-27 11:03 2.1K netMm10.txt.gz 2013-10-27 11:03 56M netMm39.sql 2020-11-26 02:59 2.1K netMm39.txt.gz 2020-11-26 02:59 56M netMonDom4.sql 2008-06-05 13:43 2.2K netMonDom4.txt.gz 2008-06-05 13:44 30M netOryCun2.sql 2010-05-02 11:41 2.0K netOryCun2.txt.gz 2010-05-02 11:41 64M netRn6.sql 2017-03-26 17:42 2.1K netRn6.txt.gz 2017-03-26 17:43 56M nscanGene.sql 2008-06-05 13:44 1.9K nscanGene.txt.gz 2008-06-05 13:44 2.1M nscanPep.sql 2008-06-05 13:44 1.1K nscanPep.txt.gz 2008-06-05 13:44 6.8M quality.sql 2008-06-05 13:44 1.7K quality.txt.gz 2008-06-05 13:46 47M refFlat.sql 2020-08-18 13:15 1.7K refFlat.txt.gz 2020-08-18 13:15 37K refGene.sql 2020-08-18 13:15 1.9K refGene.txt.gz 2020-08-18 13:15 40K refSeqAli.sql 2018-04-08 05:33 2.1K refSeqAli.txt.gz 2018-04-08 05:33 43K rmsk.sql 2008-06-05 13:46 1.9K rmsk.txt.gz 2008-06-05 13:48 99M seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 681K simpleRepeat.sql 2008-06-05 13:49 1.9K simpleRepeat.txt.gz 2008-06-05 13:49 16M tRNAs.sql 2012-04-22 20:01 1.7K tRNAs.txt.gz 2012-04-22 20:01 11K tableDescriptions.sql 2021-03-13 06:37 1.4K tableDescriptions.txt.gz 2021-03-13 06:37 7.3K tableList.sql 2021-05-02 03:10 1.6K tableList.txt.gz 2021-05-02 03:10 4.7K trackDb.sql 2021-03-26 09:06 2.1K trackDb.txt.gz 2021-03-26 09:06 51K ucscToRefSeq.sql 2018-02-18 05:44 1.4K ucscToRefSeq.txt.gz 2018-02-18 05:44 25K windowmaskerSdust.sql 2008-06-05 13:49 1.4K windowmaskerSdust.txt.gz 2008-06-05 13:51 138M xenoMrna.sql 2020-08-18 13:10 2.1K xenoMrna.txt.gz 2020-08-18 13:10 328M xenoRefFlat.sql 2020-08-18 13:30 1.7K xenoRefFlat.txt.gz 2020-08-18 13:30 32M xenoRefGene.sql 2020-08-18 13:30 1.9K xenoRefGene.txt.gz 2020-08-18 13:30 35M xenoRefSeqAli.sql 2020-08-18 13:30 2.1K xenoRefSeqAli.txt.gz 2020-08-18 13:30 35M