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 - bigFiles.txt.gz 2024-04-14 03:26 73 ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 extNcbiRefSeq.txt.gz 2020-05-10 03:26 91 grp.txt.gz 2014-03-02 03:40 208 history.txt.gz 2008-06-05 13:36 727 nscanPep.sql 2008-06-05 13:44 1.1K genscanPep.sql 2008-06-05 13:36 1.2K chromInfo.sql 2008-06-05 13:34 1.2K ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K hgFindSpec.txt.gz 2024-01-31 15:13 1.3K ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.3K ensPep.sql 2021-05-25 14:25 1.3K ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ensemblSource.sql 2021-05-25 14:25 1.4K bigFiles.sql 2024-04-14 03:26 1.4K windowmaskerSdust.sql 2008-06-05 13:49 1.4K grp.sql 2014-03-02 03:40 1.4K ensemblToGeneName.sql 2021-05-25 14:23 1.4K chainGalGal3Link.sql 2008-06-05 11:25 1.4K chromAlias.sql 2018-02-18 05:44 1.4K history.sql 2008-06-05 13:36 1.4K tableDescriptions.sql 2024-04-13 02:03 1.4K ucscToRefSeq.sql 2018-02-18 05:44 1.4K extNcbiRefSeq.sql 2020-05-10 03:26 1.4K ensGtp.sql 2021-05-25 14:23 1.4K genscanSubopt.sql 2008-06-05 13:36 1.5K chainMonDom4Link.sql 2008-06-05 12:27 1.5K chainOryCun2Link.sql 2010-05-02 11:25 1.5K microsat.sql 2015-08-23 11:56 1.5K gap.sql 2008-06-05 13:34 1.5K cytoBandIdeo.sql 2013-04-28 11:40 1.5K chainRn6Link.sql 2017-03-26 17:13 1.5K chainMm10Link.sql 2013-10-27 10:59 1.5K seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K chainGalVar1Link.sql 2016-09-18 07:11 1.5K chainMm39Link.sql 2020-11-26 02:56 1.6K tableList.sql 2024-04-14 03:26 1.6K genscan.sql 2008-06-05 13:36 1.6K chainHg19Link.sql 2009-09-20 08:12 1.6K gold.sql 2008-06-05 13:36 1.6K gbLoaded.sql 2020-08-18 13:30 1.6K cpgIslandExt.sql 2008-06-05 13:34 1.6K chainOryCun2.sql 2010-05-02 11:22 1.6K chainGalGal3.sql 2008-06-05 11:25 1.7K chainMonDom4.sql 2008-06-05 12:18 1.7K tRNAs.sql 2012-04-22 20:01 1.7K chainRn6.sql 2017-03-26 17:10 1.7K chainMm10.sql 2013-10-27 10:59 1.7K chainGalVar1.sql 2016-09-18 07:08 1.7K cpgIslandExtUnmasked.sql 2014-06-01 09:51 1.7K gc5Base.sql 2008-06-05 13:36 1.7K quality.sql 2008-06-05 13:44 1.7K chainMm39.sql 2020-11-26 02:53 1.7K refFlat.sql 2020-08-18 13:15 1.7K xenoRefFlat.sql 2020-08-18 13:30 1.7K hgFindSpec.sql 2024-01-31 15:13 1.8K estOrientInfo.sql 2016-06-26 06:05 1.8K chainHg19.sql 2009-09-20 08:28 1.8K hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K mrnaOrientInfo.sql 2020-05-06 01:22 1.8K rmsk.sql 2008-06-05 13:46 1.9K nscanGene.sql 2008-06-05 13:44 1.9K nestedRepeats.sql 2008-06-05 13:38 1.9K simpleRepeat.sql 2008-06-05 13:49 1.9K ncbiRefSeq.sql 2020-05-10 03:26 1.9K augustusGene.sql 2015-07-26 11:11 1.9K ensGene.sql 2021-05-25 14:23 1.9K refGene.sql 2020-08-18 13:15 1.9K ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K xenoRefGene.sql 2020-08-18 13:30 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K netOryCun2.sql 2010-05-02 11:41 2.0K trackDb.sql 2024-01-31 15:13 2.1K netRn6.sql 2017-03-26 17:42 2.1K trackDb_pushedout.sql 2023-12-05 13:51 2.1K netMm10.sql 2013-10-27 11:03 2.1K netGalVar1.sql 2016-09-18 07:23 2.1K all_est.sql 2016-06-26 06:05 2.1K intronEst.sql 2016-06-26 06:05 2.1K refSeqAli.sql 2018-04-08 05:33 2.1K netMm39.sql 2020-11-26 02:59 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K all_mrna.sql 2020-05-06 01:22 2.1K xenoMrna.sql 2020-08-18 13:10 2.1K xenoRefSeqAli.sql 2020-08-18 13:30 2.1K netGalGal3.sql 2008-06-05 13:39 2.2K netMonDom4.sql 2008-06-05 13:43 2.2K blastHg18KG.sql 2009-12-20 10:45 2.3K netHg19.sql 2009-09-20 08:12 2.3K tableList.txt.gz 2024-04-14 03:26 4.9K tableDescriptions.txt.gz 2024-04-13 02:03 7.3K tRNAs.txt.gz 2012-04-22 20:01 11K cytoBandIdeo.txt.gz 2013-04-28 11:40 18K chromInfo.txt.gz 2008-06-05 13:34 18K ucscToRefSeq.txt.gz 2018-02-18 05:44 25K chromAlias.txt.gz 2018-02-18 05:44 29K refFlat.txt.gz 2020-08-18 13:15 37K refGene.txt.gz 2020-08-18 13:15 40K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 40K trackDb_pushedout.txt.gz 2023-12-05 13:51 41K refSeqAli.txt.gz 2018-04-08 05:33 43K trackDb.txt.gz 2024-01-31 15:13 57K mrnaOrientInfo.txt.gz 2020-05-06 01:22 101K ensemblSource.txt.gz 2021-05-25 14:25 105K gbLoaded.txt.gz 2020-08-18 13:30 113K ensemblToGeneName.txt.gz 2021-05-25 14:23 171K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 255K all_mrna.txt.gz 2020-05-06 01:22 298K estOrientInfo.txt.gz 2016-06-26 06:05 341K ensGtp.txt.gz 2021-05-25 14:23 348K intronEst.txt.gz 2016-06-26 06:05 534K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 681K microsat.txt.gz 2015-08-23 11:56 748K gap.txt.gz 2008-06-05 13:34 819K cpgIslandExt.txt.gz 2008-06-05 13:34 820K cpgIslandExtUnmasked.txt.gz 2014-06-01 09:51 841K all_est.txt.gz 2016-06-26 06:05 1.1M gold.txt.gz 2008-06-05 13:36 1.1M ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.3M nscanGene.txt.gz 2008-06-05 13:44 2.1M ensGene.txt.gz 2021-05-25 14:23 2.4M augustusGene.txt.gz 2015-07-26 11:11 2.7M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.8M ncbiRefSeq.txt.gz 2020-05-10 03:26 2.8M ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.3M blastHg18KG.txt.gz 2009-12-20 10:45 3.5M genscan.txt.gz 2008-06-05 13:36 4.2M genscanSubopt.txt.gz 2008-06-05 13:36 6.4M nscanPep.txt.gz 2008-06-05 13:44 6.8M ensPep.txt.gz 2021-05-25 14:25 8.2M nestedRepeats.txt.gz 2008-06-05 13:39 9.1M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 9.2M gc5Base.txt.gz 2008-06-05 13:36 11M netGalGal3.txt.gz 2008-06-05 13:39 13M genscanPep.txt.gz 2008-06-05 13:36 15M simpleRepeat.txt.gz 2008-06-05 13:49 16M chainGalGal3.txt.gz 2008-06-05 11:25 27M netMonDom4.txt.gz 2008-06-05 13:44 30M xenoRefFlat.txt.gz 2020-08-18 13:30 32M xenoRefGene.txt.gz 2020-08-18 13:30 35M xenoRefSeqAli.txt.gz 2020-08-18 13:30 35M quality.txt.gz 2008-06-05 13:46 47M netRn6.txt.gz 2017-03-26 17:43 56M netMm39.txt.gz 2020-11-26 02:59 56M netMm10.txt.gz 2013-10-27 11:03 56M netHg19.txt.gz 2009-09-20 08:12 57M chainMm39.txt.gz 2020-11-26 02:53 62M netOryCun2.txt.gz 2010-05-02 11:41 64M netGalVar1.txt.gz 2016-09-18 07:23 65M chainRn6.txt.gz 2017-03-26 17:11 81M rmsk.txt.gz 2008-06-05 13:48 99M chainMm10.txt.gz 2013-10-27 10:59 111M windowmaskerSdust.txt.gz 2008-06-05 13:51 138M chainGalGal3Link.txt.gz 2008-06-05 11:28 191M xenoMrna.txt.gz 2020-08-18 13:10 328M chainMonDom4.txt.gz 2008-06-05 12:22 385M chainMm39Link.txt.gz 2020-11-26 02:56 506M chainOryCun2.txt.gz 2010-05-02 11:23 518M chainHg19.txt.gz 2009-09-20 08:30 570M chainRn6Link.txt.gz 2017-03-26 17:21 607M chainGalVar1.txt.gz 2016-09-18 07:09 701M chainMm10Link.txt.gz 2013-10-27 11:00 706M chainMonDom4Link.txt.gz 2008-06-05 12:49 1.8G chainOryCun2Link.txt.gz 2010-05-02 11:30 2.0G chainHg19Link.txt.gz 2009-09-20 08:17 2.1G chainGalVar1Link.txt.gz 2016-09-18 07:14 2.1G