This directory contains a dump of the UCSC genome annotation database for the
    Jun. 2017 (ASM220157v1/neoSch1) assembly of the hawaiian monk seal genome
    (neoSch1, Johns Hopkins University) .

The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    https://www.ncbi.nlm.nih.gov/genome/8042
    https://www.ncbi.nlm.nih.gov/genome/assembly/1137021
    https://www.ncbi.nlm.nih.gov/bioproject/384558

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=neoSch1
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/neoSch1/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/neoSch1/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/neoSch1/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/neoSch1/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/neoSch1/database/gc5Base.txt.gz' 
        -O gc5Base.txt.gz

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 neoSch1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql neoSch1 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

-----------------------------------------------------------------------------
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 - cpgIslandExtUnmasked.sql 2017-09-22 13:49 1.7K cpgIslandExtUnmasked.txt.gz 2017-09-22 13:49 1.1M simpleRepeat.sql 2017-09-22 13:53 1.9K simpleRepeat.txt.gz 2017-09-22 13:53 14M gc5BaseBw.sql 2017-09-22 14:34 1.3K gc5BaseBw.txt.gz 2017-09-22 14:34 66 grp.sql 2017-09-22 14:34 1.3K grp.txt.gz 2017-09-22 14:34 213 cytoBandIdeo.sql 2017-09-22 14:34 1.5K cytoBandIdeo.txt.gz 2017-09-22 14:34 41K chromInfo.sql 2017-09-22 14:34 1.4K chromInfo.txt.gz 2017-09-22 14:34 41K rmsk.sql 2017-09-22 17:55 1.9K rmsk.txt.gz 2017-09-22 17:55 120M nestedRepeats.sql 2017-09-22 17:58 1.9K nestedRepeats.txt.gz 2017-09-22 17:58 14M microsat.sql 2017-09-22 20:42 1.5K microsat.txt.gz 2017-09-22 20:42 260K chromAlias.sql 2017-09-22 20:53 1.4K chromAlias.txt.gz 2017-09-22 20:53 83K windowmaskerSdust.sql 2017-09-22 23:16 1.5K windowmaskerSdust.txt.gz 2017-09-22 23:16 129M ucscToRefSeq.sql 2017-09-23 01:44 1.4K ucscToRefSeq.txt.gz 2017-09-23 01:44 58K ucscToINSDC.sql 2017-09-23 01:44 1.4K ucscToINSDC.txt.gz 2017-09-23 01:44 66K cpgIslandExt.sql 2017-09-25 10:22 1.7K cpgIslandExt.txt.gz 2017-09-25 10:22 1.0M augustusGene.sql 2017-09-25 13:46 1.9K augustusGene.txt.gz 2017-09-25 13:46 2.2M genscan.sql 2017-10-06 09:39 1.7K genscan.txt.gz 2017-10-06 09:39 3.0M chainMm10.sql 2018-03-16 09:18 1.7K chainMm10.txt.gz 2018-03-16 09:18 46M chainMm10Link.sql 2018-03-16 09:23 1.5K chainMm10Link.txt.gz 2018-03-16 09:23 413M netMm10.sql 2018-03-16 09:28 2.1K netMm10.txt.gz 2018-03-16 09:28 63M chainSynMm10.sql 2018-03-16 09:37 1.7K chainSynMm10.txt.gz 2018-03-16 09:37 224K chainSynMm10Link.sql 2018-03-16 09:41 1.5K chainSynMm10Link.txt.gz 2018-03-16 09:41 238M netSynMm10.sql 2018-03-16 09:42 2.1K netSynMm10.txt.gz 2018-03-16 09:42 60M chainHg38.sql 2018-03-16 09:44 1.7K chainHg38.txt.gz 2018-03-16 09:44 231M chainHg38Link.sql 2018-03-16 09:56 1.5K chainHg38Link.txt.gz 2018-03-16 09:56 906M netHg38.sql 2018-03-16 10:00 2.1K netHg38.txt.gz 2018-03-16 10:00 60M chainSynHg38.sql 2018-03-16 10:17 1.7K chainSynHg38.txt.gz 2018-03-16 10:17 446K chainSynHg38Link.sql 2018-03-16 10:22 1.5K chainSynHg38Link.txt.gz 2018-03-16 10:22 316M netSynHg38.sql 2018-03-16 10:23 2.1K netSynHg38.txt.gz 2018-03-16 10:23 57M chainRBestMm10.sql 2018-03-16 15:18 1.7K chainRBestMm10.txt.gz 2018-03-16 15:18 916K chainRBestMm10Link.sql 2018-03-16 15:22 1.6K chainRBestMm10Link.txt.gz 2018-03-16 15:22 242M netRBestMm10.sql 2018-03-16 15:29 2.1K netRBestMm10.txt.gz 2018-03-16 15:29 62M chainRBestHg38.sql 2018-03-16 17:54 1.7K chainRBestHg38.txt.gz 2018-03-16 17:54 1.4M chainRBestHg38Link.sql 2018-03-16 17:58 1.6K chainRBestHg38Link.txt.gz 2018-03-16 17:58 320M netRBestHg38.sql 2018-03-16 18:03 2.1K netRBestHg38.txt.gz 2018-03-16 18:03 60M ncbiRefSeq.sql 2020-04-01 11:42 1.9K ncbiRefSeq.txt.gz 2020-04-01 11:42 2.3M ncbiRefSeqCurated.sql 2020-04-01 11:42 2.0K ncbiRefSeqCurated.txt.gz 2020-04-01 11:42 328 ncbiRefSeqPredicted.sql 2020-04-01 11:42 2.0K ncbiRefSeqPredicted.txt.gz 2020-04-01 11:42 2.3M ncbiRefSeqLink.sql 2020-04-01 11:42 2.0K ncbiRefSeqLink.txt.gz 2020-04-01 11:42 848K ncbiRefSeqPsl.sql 2020-04-01 11:42 2.1K ncbiRefSeqPsl.txt.gz 2020-04-01 11:42 2.6M extNcbiRefSeq.sql 2020-04-01 12:00 1.4K ncbiRefSeqCds.sql 2020-04-01 12:00 1.3K ncbiRefSeqOther.sql 2020-04-01 12:00 1.3K ncbiRefSeqPepTable.sql 2020-04-01 12:00 1.4K seqNcbiRefSeq.sql 2020-04-01 12:00 1.5K ncbiRefSeqOther.txt.gz 2020-04-01 12:00 75 ncbiRefSeqCds.txt.gz 2020-04-01 12:00 181K extNcbiRefSeq.txt.gz 2020-04-01 12:00 90 ncbiRefSeqPepTable.txt.gz 2020-04-01 12:00 6.3M seqNcbiRefSeq.txt.gz 2020-04-01 12:00 453K chainRheMac10.sql 2020-07-12 06:42 1.7K chainRheMac10.txt.gz 2020-07-12 06:42 204M chainRheMac10Link.sql 2020-07-12 06:49 1.6K chainRheMac10Link.txt.gz 2020-07-12 06:49 840M netRheMac10.sql 2020-07-12 06:52 2.1K netRheMac10.txt.gz 2020-07-12 06:52 61M chainSynRheMac10.sql 2020-07-12 07:03 1.7K chainSynRheMac10.txt.gz 2020-07-12 07:03 437K chainSynRheMac10Link.sql 2020-07-12 07:06 1.6K chainSynRheMac10Link.txt.gz 2020-07-12 07:06 318M netSynRheMac10.sql 2020-07-12 07:07 2.1K netSynRheMac10.txt.gz 2020-07-12 07:07 57M chainRBestRheMac10.sql 2020-07-12 10:39 1.7K chainRBestRheMac10.txt.gz 2020-07-12 10:39 1.4M chainRBestRheMac10Link.sql 2020-07-12 10:41 1.6K chainRBestRheMac10Link.txt.gz 2020-07-12 10:41 322M netRBestRheMac10.sql 2020-07-12 10:45 2.1K netRBestRheMac10.txt.gz 2020-07-12 10:45 61M chainPanTro6.sql 2020-07-12 11:36 1.7K chainPanTro6.txt.gz 2020-07-12 11:36 225M chainPanTro6Link.sql 2020-07-12 11:43 1.5K chainPanTro6Link.txt.gz 2020-07-12 11:43 873M netPanTro6.sql 2020-07-12 11:46 2.1K netPanTro6.txt.gz 2020-07-12 11:46 60M chainSynPanTro6.sql 2020-07-12 11:58 1.7K chainSynPanTro6.txt.gz 2020-07-12 11:58 442K chainSynPanTro6Link.sql 2020-07-12 12:01 1.6K chainSynPanTro6Link.txt.gz 2020-07-12 12:01 316M netSynPanTro6.sql 2020-07-12 12:02 2.1K netSynPanTro6.txt.gz 2020-07-12 12:02 57M chainRBestPanTro6.sql 2020-07-12 15:48 1.7K chainRBestPanTro6.txt.gz 2020-07-12 15:48 1.4M chainRBestPanTro6Link.sql 2020-07-12 15:50 1.6K chainRBestPanTro6Link.txt.gz 2020-07-12 15:50 319M netRBestPanTro6.sql 2020-07-12 15:54 2.1K netRBestPanTro6.txt.gz 2020-07-12 15:54 60M chainCanFam4.sql 2020-07-14 04:16 1.7K chainCanFam4.txt.gz 2020-07-14 04:16 400M chainCanFam4Link.sql 2020-07-14 04:36 1.5K chainCanFam4Link.txt.gz 2020-07-14 04:36 1.9G netCanFam4.sql 2020-07-14 04:39 2.1K netCanFam4.txt.gz 2020-07-14 04:39 51M chainSynCanFam4.sql 2020-07-14 05:01 1.7K chainSynCanFam4.txt.gz 2020-07-14 05:01 761K chainSynCanFam4Link.sql 2020-07-14 05:04 1.6K chainSynCanFam4Link.txt.gz 2020-07-14 05:04 252M netSynCanFam4.sql 2020-07-14 05:04 2.1K netSynCanFam4.txt.gz 2020-07-14 05:04 46M chainRBestCanFam4.sql 2020-07-14 08:28 1.7K chainRBestCanFam4.txt.gz 2020-07-14 08:28 2.0M chainRBestCanFam4Link.sql 2020-07-14 08:30 1.6K chainRBestCanFam4Link.txt.gz 2020-07-14 08:30 256M netRBestCanFam4.sql 2020-07-14 08:33 2.1K netRBestCanFam4.txt.gz 2020-07-14 08:33 50M chainLoxAfr3.sql 2020-07-15 18:16 1.7K chainLoxAfr3.txt.gz 2020-07-15 18:16 199M chainLoxAfr3Link.sql 2020-07-15 18:23 1.5K chainLoxAfr3Link.txt.gz 2020-07-15 18:23 881M netLoxAfr3.sql 2020-07-15 18:25 2.1K netLoxAfr3.txt.gz 2020-07-15 18:25 62M chainSynLoxAfr3.sql 2020-07-15 18:38 1.7K chainSynLoxAfr3.txt.gz 2020-07-15 18:38 436K chainSynLoxAfr3Link.sql 2020-07-15 18:40 1.6K chainSynLoxAfr3Link.txt.gz 2020-07-15 18:40 287M netSynLoxAfr3.sql 2020-07-15 18:41 2.1K netSynLoxAfr3.txt.gz 2020-07-15 18:41 59M chainRBestLoxAfr3.sql 2020-07-15 20:52 1.7K chainRBestLoxAfr3.txt.gz 2020-07-15 20:52 1.5M chainRBestLoxAfr3Link.sql 2020-07-15 20:54 1.6K chainRBestLoxAfr3Link.txt.gz 2020-07-15 20:54 291M netRBestLoxAfr3.sql 2020-07-15 20:57 2.1K netRBestLoxAfr3.txt.gz 2020-07-15 20:57 62M chainOrnAna2.sql 2020-07-16 15:53 1.7K chainOrnAna2.txt.gz 2020-07-16 15:53 54M chainOrnAna2Link.sql 2020-07-16 15:55 1.5K chainOrnAna2Link.txt.gz 2020-07-16 15:55 314M netOrnAna2.sql 2020-07-16 15:56 2.1K netOrnAna2.txt.gz 2020-07-16 15:56 20M chainSynOrnAna2.sql 2020-07-16 16:06 1.7K chainSynOrnAna2.txt.gz 2020-07-16 16:06 170K chainSynOrnAna2Link.sql 2020-07-16 16:06 1.6K chainSynOrnAna2Link.txt.gz 2020-07-16 16:06 32M netSynOrnAna2.sql 2020-07-16 16:06 2.1K netSynOrnAna2.txt.gz 2020-07-16 16:06 9.4M chainRBestOrnAna2.sql 2020-07-16 17:14 1.7K chainRBestOrnAna2.txt.gz 2020-07-16 17:14 2.9M chainRBestOrnAna2Link.sql 2020-07-16 17:14 1.6K chainRBestOrnAna2Link.txt.gz 2020-07-16 17:14 49M netRBestOrnAna2.sql 2020-07-16 17:16 2.1K netRBestOrnAna2.txt.gz 2020-07-16 17:16 20M chainMonDom5.sql 2020-07-16 19:26 1.7K chainMonDom5.txt.gz 2020-07-16 19:26 306M chainMonDom5Link.sql 2020-07-16 19:36 1.5K chainMonDom5Link.txt.gz 2020-07-16 19:36 1.1G netMonDom5.sql 2020-07-16 19:38 2.1K netMonDom5.txt.gz 2020-07-16 19:38 28M chainSynMonDom5.sql 2020-07-16 19:51 1.7K chainSynMonDom5.txt.gz 2020-07-16 19:51 235K chainSynMonDom5Link.sql 2020-07-16 19:51 1.6K chainSynMonDom5Link.txt.gz 2020-07-16 19:51 81M netSynMonDom5.sql 2020-07-16 19:51 2.1K netSynMonDom5.txt.gz 2020-07-16 19:51 20M chainRBestMonDom5.sql 2020-07-17 09:59 1.7K chainRBestMonDom5.txt.gz 2020-07-17 09:59 2.5M chainRBestMonDom5Link.sql 2020-07-17 10:00 1.6K chainRBestMonDom5Link.txt.gz 2020-07-17 10:00 96M netRBestMonDom5.sql 2020-07-17 10:02 2.1K netRBestMonDom5.txt.gz 2020-07-17 10:02 29M xenoRefFlat.sql 2020-08-19 20:39 1.7K xenoRefGene.sql 2020-08-19 20:39 1.9K xenoRefSeqAli.sql 2020-08-19 20:39 2.1K xenoRefGene.txt.gz 2020-08-19 20:39 39M xenoRefFlat.txt.gz 2020-08-19 20:39 35M xenoRefSeqAli.txt.gz 2020-08-19 20:39 38M gbLoaded.sql 2020-08-19 20:54 1.6K gbLoaded.txt.gz 2020-08-19 20:54 3.9K gold.sql 2020-09-11 13:52 1.7K gold.txt.gz 2020-09-11 13:52 821K gap.sql 2020-09-11 13:52 1.6K gap.txt.gz 2020-09-11 13:52 499K history.sql 2020-09-11 16:38 1.6K history.txt.gz 2020-09-11 16:38 1.7K chainMm39.sql 2020-11-25 01:56 1.7K chainMm39.txt.gz 2020-11-25 01:56 44M chainMm39Link.sql 2020-11-25 02:00 1.6K chainMm39Link.txt.gz 2020-11-25 02:00 404M netMm39.sql 2020-11-25 02:03 2.1K netMm39.txt.gz 2020-11-25 02:03 63M tableDescriptions.sql 2021-03-13 06:37 1.4K tableDescriptions.txt.gz 2021-03-13 06:37 7.6K trackDb.sql 2021-08-02 14:30 2.1K trackDb.txt.gz 2021-08-02 14:30 35K hgFindSpec.sql 2021-08-02 14:30 1.8K hgFindSpec.txt.gz 2021-08-02 14:30 946 tableList.sql 2022-08-07 03:03 1.6K tableList.txt.gz 2022-08-07 03:03 5.9K bigFiles.sql 2022-08-07 03:03 1.4K bigFiles.txt.gz 2022-08-07 03:03 95