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.
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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.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;'
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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 -
gc5BaseBw.txt.gz 2017-09-22 14:34 66
ncbiRefSeqOther.txt.gz 2020-04-01 12:00 75
extNcbiRefSeq.txt.gz 2020-04-01 12:00 90
bigFiles.txt.gz 2024-11-17 03:13 95
grp.txt.gz 2017-09-22 14:34 213
ncbiRefSeqCurated.txt.gz 2020-04-01 11:42 328
hgFindSpec.txt.gz 2024-01-31 15:13 1.0K
gc5BaseBw.sql 2017-09-22 14:34 1.3K
ncbiRefSeqOther.sql 2020-04-01 12:00 1.3K
ncbiRefSeqCds.sql 2020-04-01 12:00 1.4K
grp.sql 2017-09-22 14:34 1.4K
ncbiRefSeqPepTable.sql 2020-04-01 12:00 1.4K
bigFiles.sql 2024-11-17 03:13 1.4K
chromInfo.sql 2017-09-22 14:34 1.4K
chromAlias.sql 2017-09-22 20:53 1.4K
ucscToINSDC.sql 2017-09-23 01:44 1.4K
ucscToRefSeq.sql 2017-09-23 01:44 1.5K
tableDescriptions.sql 2024-11-16 02:04 1.5K
extNcbiRefSeq.sql 2020-04-01 12:00 1.5K
microsat.sql 2017-09-22 20:42 1.5K
windowmaskerSdust.sql 2017-09-22 23:16 1.5K
cytoBandIdeo.sql 2017-09-22 14:34 1.5K
chainHg38Link.sql 2018-03-16 09:56 1.6K
chainMm10Link.sql 2018-03-16 09:23 1.6K
chainMm39Link.sql 2020-11-25 02:00 1.6K
seqNcbiRefSeq.sql 2020-04-01 12:00 1.6K
chainCanFam4Link.sql 2020-07-14 04:36 1.6K
chainLoxAfr3Link.sql 2020-07-15 18:23 1.6K
chainMonDom5Link.sql 2020-07-16 19:36 1.6K
chainOrnAna2Link.sql 2020-07-16 15:55 1.6K
chainPanTro6Link.sql 2020-07-12 11:43 1.6K
chainSynHg38Link.sql 2018-03-16 10:22 1.6K
chainSynMm10Link.sql 2018-03-16 09:41 1.6K
chainRheMac10Link.sql 2020-07-12 06:49 1.6K
chainRBestHg38Link.sql 2018-03-16 17:58 1.6K
chainRBestMm10Link.sql 2018-03-16 15:22 1.6K
chainSynCanFam4Link.sql 2020-07-14 05:04 1.6K
chainSynLoxAfr3Link.sql 2020-07-15 18:40 1.6K
chainSynMonDom5Link.sql 2020-07-16 19:51 1.6K
chainSynOrnAna2Link.sql 2020-07-16 16:06 1.6K
chainSynPanTro6Link.sql 2020-07-12 12:01 1.6K
chainSynRheMac10Link.sql 2020-07-12 07:06 1.6K
chainRBestCanFam4Link.sql 2020-07-14 08:30 1.6K
chainRBestLoxAfr3Link.sql 2020-07-15 20:54 1.6K
chainRBestMonDom5Link.sql 2020-07-17 10:00 1.6K
chainRBestOrnAna2Link.sql 2020-07-16 17:14 1.6K
chainRBestPanTro6Link.sql 2020-07-12 15:50 1.6K
chainRBestRheMac10Link.sql 2020-07-12 10:41 1.6K
tableList.sql 2024-11-17 03:13 1.6K
history.sql 2020-09-11 16:38 1.6K
gbLoaded.sql 2020-08-19 20:54 1.6K
gap.sql 2020-09-11 13:52 1.6K
history.txt.gz 2020-09-11 16:38 1.7K
gold.sql 2020-09-11 13:52 1.7K
genscan.sql 2017-10-06 09:39 1.7K
cpgIslandExt.sql 2017-09-25 10:22 1.7K
chainHg38.sql 2018-03-16 09:44 1.7K
chainMm10.sql 2018-03-16 09:18 1.7K
chainMm39.sql 2020-11-25 01:56 1.7K
chainCanFam4.sql 2020-07-14 04:16 1.7K
chainLoxAfr3.sql 2020-07-15 18:16 1.7K
chainMonDom5.sql 2020-07-16 19:26 1.7K
chainOrnAna2.sql 2020-07-16 15:53 1.7K
chainPanTro6.sql 2020-07-12 11:36 1.7K
chainSynHg38.sql 2018-03-16 10:17 1.7K
chainSynMm10.sql 2018-03-16 09:37 1.7K
cpgIslandExtUnmasked.sql 2017-09-22 13:49 1.7K
chainRheMac10.sql 2020-07-12 06:42 1.7K
chainRBestHg38.sql 2018-03-16 17:54 1.7K
chainRBestMm10.sql 2018-03-16 15:18 1.7K
chainSynCanFam4.sql 2020-07-14 05:01 1.7K
chainSynLoxAfr3.sql 2020-07-15 18:38 1.7K
chainSynMonDom5.sql 2020-07-16 19:51 1.7K
chainSynOrnAna2.sql 2020-07-16 16:06 1.7K
chainSynPanTro6.sql 2020-07-12 11:58 1.7K
xenoRefFlat.sql 2020-08-19 20:39 1.7K
chainSynRheMac10.sql 2020-07-12 07:03 1.8K
chainRBestCanFam4.sql 2020-07-14 08:28 1.8K
chainRBestLoxAfr3.sql 2020-07-15 20:52 1.8K
chainRBestMonDom5.sql 2020-07-17 09:59 1.8K
chainRBestOrnAna2.sql 2020-07-16 17:14 1.8K
chainRBestPanTro6.sql 2020-07-12 15:48 1.8K
chainRBestRheMac10.sql 2020-07-12 10:39 1.8K
hgFindSpec.sql 2024-01-31 15:13 1.8K
rmsk.sql 2017-09-22 17:55 1.9K
simpleRepeat.sql 2017-09-22 13:53 1.9K
ncbiRefSeq.sql 2020-04-01 11:42 2.0K
nestedRepeats.sql 2017-09-22 17:58 2.0K
xenoRefGene.sql 2020-08-19 20:39 2.0K
augustusGene.sql 2017-09-25 13:46 2.0K
ncbiRefSeqCurated.sql 2020-04-01 11:42 2.0K
ncbiRefSeqPredicted.sql 2020-04-01 11:42 2.0K
ncbiRefSeqLink.sql 2020-04-01 11:42 2.0K
trackDb.sql 2024-01-31 15:13 2.1K
netHg38.sql 2018-03-16 10:00 2.1K
netMm10.sql 2018-03-16 09:28 2.1K
netMm39.sql 2020-11-25 02:03 2.1K
netCanFam4.sql 2020-07-14 04:39 2.1K
netLoxAfr3.sql 2020-07-15 18:25 2.1K
netMonDom5.sql 2020-07-16 19:38 2.1K
netOrnAna2.sql 2020-07-16 15:56 2.1K
netPanTro6.sql 2020-07-12 11:46 2.1K
netSynHg38.sql 2018-03-16 10:23 2.1K
netSynMm10.sql 2018-03-16 09:42 2.1K
netRheMac10.sql 2020-07-12 06:52 2.1K
netRBestHg38.sql 2018-03-16 18:03 2.1K
netRBestMm10.sql 2018-03-16 15:29 2.1K
netSynCanFam4.sql 2020-07-14 05:04 2.1K
netSynLoxAfr3.sql 2020-07-15 18:41 2.1K
netSynMonDom5.sql 2020-07-16 19:51 2.1K
netSynOrnAna2.sql 2020-07-16 16:06 2.1K
netSynPanTro6.sql 2020-07-12 12:02 2.1K
netSynRheMac10.sql 2020-07-12 07:07 2.1K
netRBestCanFam4.sql 2020-07-14 08:33 2.1K
netRBestLoxAfr3.sql 2020-07-15 20:57 2.1K
netRBestMonDom5.sql 2020-07-17 10:02 2.1K
netRBestOrnAna2.sql 2020-07-16 17:16 2.1K
netRBestPanTro6.sql 2020-07-12 15:54 2.1K
netRBestRheMac10.sql 2020-07-12 10:45 2.1K
ncbiRefSeqPsl.sql 2020-04-01 11:42 2.1K
xenoRefSeqAli.sql 2020-08-19 20:39 2.1K
gbLoaded.txt.gz 2020-08-19 20:54 3.9K
tableList.txt.gz 2024-11-17 03:13 5.8K
tableDescriptions.txt.gz 2024-11-16 02:04 7.6K
chromInfo.txt.gz 2017-09-22 14:34 41K
cytoBandIdeo.txt.gz 2017-09-22 14:34 41K
trackDb.txt.gz 2024-01-31 15:13 46K
ucscToRefSeq.txt.gz 2017-09-23 01:44 58K
ucscToINSDC.txt.gz 2017-09-23 01:44 66K
chromAlias.txt.gz 2017-09-22 20:53 83K
chainSynOrnAna2.txt.gz 2020-07-16 16:06 170K
ncbiRefSeqCds.txt.gz 2020-04-01 12:00 181K
chainSynMm10.txt.gz 2018-03-16 09:37 224K
chainSynMonDom5.txt.gz 2020-07-16 19:51 235K
microsat.txt.gz 2017-09-22 20:42 260K
chainSynLoxAfr3.txt.gz 2020-07-15 18:38 436K
chainSynRheMac10.txt.gz 2020-07-12 07:03 437K
chainSynPanTro6.txt.gz 2020-07-12 11:58 442K
chainSynHg38.txt.gz 2018-03-16 10:17 446K
seqNcbiRefSeq.txt.gz 2020-04-01 12:00 453K
gap.txt.gz 2020-09-11 13:52 499K
chainSynCanFam4.txt.gz 2020-07-14 05:01 761K
gold.txt.gz 2020-09-11 13:52 821K
ncbiRefSeqLink.txt.gz 2020-04-01 11:42 848K
chainRBestMm10.txt.gz 2018-03-16 15:18 916K
cpgIslandExt.txt.gz 2017-09-25 10:22 1.0M
cpgIslandExtUnmasked.txt.gz 2017-09-22 13:49 1.1M
chainRBestRheMac10.txt.gz 2020-07-12 10:39 1.4M
chainRBestPanTro6.txt.gz 2020-07-12 15:48 1.4M
chainRBestHg38.txt.gz 2018-03-16 17:54 1.4M
chainRBestLoxAfr3.txt.gz 2020-07-15 20:52 1.5M
chainRBestCanFam4.txt.gz 2020-07-14 08:28 2.0M
augustusGene.txt.gz 2017-09-25 13:46 2.2M
ncbiRefSeqPredicted.txt.gz 2020-04-01 11:42 2.3M
ncbiRefSeq.txt.gz 2020-04-01 11:42 2.3M
chainRBestMonDom5.txt.gz 2020-07-17 09:59 2.5M
ncbiRefSeqPsl.txt.gz 2020-04-01 11:42 2.6M
chainRBestOrnAna2.txt.gz 2020-07-16 17:14 2.9M
genscan.txt.gz 2017-10-06 09:39 3.0M
ncbiRefSeqPepTable.txt.gz 2020-04-01 12:00 6.3M
netSynOrnAna2.txt.gz 2020-07-16 16:06 9.4M
nestedRepeats.txt.gz 2017-09-22 17:58 14M
simpleRepeat.txt.gz 2017-09-22 13:53 14M
netSynMonDom5.txt.gz 2020-07-16 19:51 20M
netRBestOrnAna2.txt.gz 2020-07-16 17:16 20M
netOrnAna2.txt.gz 2020-07-16 15:56 20M
netMonDom5.txt.gz 2020-07-16 19:38 28M
netRBestMonDom5.txt.gz 2020-07-17 10:02 29M
chainSynOrnAna2Link.txt.gz 2020-07-16 16:06 32M
xenoRefFlat.txt.gz 2020-08-19 20:39 35M
xenoRefSeqAli.txt.gz 2020-08-19 20:39 38M
xenoRefGene.txt.gz 2020-08-19 20:39 39M
chainMm39.txt.gz 2020-11-25 01:56 44M
chainMm10.txt.gz 2018-03-16 09:18 46M
netSynCanFam4.txt.gz 2020-07-14 05:04 46M
chainRBestOrnAna2Link.txt.gz 2020-07-16 17:14 49M
netRBestCanFam4.txt.gz 2020-07-14 08:33 50M
netCanFam4.txt.gz 2020-07-14 04:39 51M
chainOrnAna2.txt.gz 2020-07-16 15:53 54M
netSynPanTro6.txt.gz 2020-07-12 12:02 57M
netSynHg38.txt.gz 2018-03-16 10:23 57M
netSynRheMac10.txt.gz 2020-07-12 07:07 57M
netSynLoxAfr3.txt.gz 2020-07-15 18:41 59M
netRBestHg38.txt.gz 2018-03-16 18:03 60M
netRBestPanTro6.txt.gz 2020-07-12 15:54 60M
netPanTro6.txt.gz 2020-07-12 11:46 60M
netHg38.txt.gz 2018-03-16 10:00 60M
netSynMm10.txt.gz 2018-03-16 09:42 60M
netRBestRheMac10.txt.gz 2020-07-12 10:45 61M
netRheMac10.txt.gz 2020-07-12 06:52 61M
netRBestMm10.txt.gz 2018-03-16 15:29 62M
netLoxAfr3.txt.gz 2020-07-15 18:25 62M
netRBestLoxAfr3.txt.gz 2020-07-15 20:57 62M
netMm10.txt.gz 2018-03-16 09:28 63M
netMm39.txt.gz 2020-11-25 02:03 63M
chainSynMonDom5Link.txt.gz 2020-07-16 19:51 81M
chainRBestMonDom5Link.txt.gz 2020-07-17 10:00 96M
rmsk.txt.gz 2017-09-22 17:55 120M
windowmaskerSdust.txt.gz 2017-09-22 23:16 129M
chainLoxAfr3.txt.gz 2020-07-15 18:16 199M
chainRheMac10.txt.gz 2020-07-12 06:42 204M
chainPanTro6.txt.gz 2020-07-12 11:36 225M
chainHg38.txt.gz 2018-03-16 09:44 231M
chainSynMm10Link.txt.gz 2018-03-16 09:41 238M
chainRBestMm10Link.txt.gz 2018-03-16 15:22 242M
chainSynCanFam4Link.txt.gz 2020-07-14 05:04 252M
chainRBestCanFam4Link.txt.gz 2020-07-14 08:30 256M
chainSynLoxAfr3Link.txt.gz 2020-07-15 18:40 287M
chainRBestLoxAfr3Link.txt.gz 2020-07-15 20:54 291M
chainMonDom5.txt.gz 2020-07-16 19:26 306M
chainOrnAna2Link.txt.gz 2020-07-16 15:55 314M
chainSynPanTro6Link.txt.gz 2020-07-12 12:01 316M
chainSynHg38Link.txt.gz 2018-03-16 10:22 316M
chainSynRheMac10Link.txt.gz 2020-07-12 07:06 318M
chainRBestPanTro6Link.txt.gz 2020-07-12 15:50 319M
chainRBestHg38Link.txt.gz 2018-03-16 17:58 320M
chainRBestRheMac10Link.txt.gz 2020-07-12 10:41 322M
chainCanFam4.txt.gz 2020-07-14 04:16 400M
chainMm39Link.txt.gz 2020-11-25 02:00 404M
chainMm10Link.txt.gz 2018-03-16 09:23 413M
chainRheMac10Link.txt.gz 2020-07-12 06:49 840M
chainPanTro6Link.txt.gz 2020-07-12 11:43 873M
chainLoxAfr3Link.txt.gz 2020-07-15 18:23 881M
chainHg38Link.txt.gz 2018-03-16 09:56 906M
chainMonDom5Link.txt.gz 2020-07-16 19:36 1.1G
chainCanFam4Link.txt.gz 2020-07-14 04:36 1.9G