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 1.4K
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 2.0K
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 1.5K
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 2.0K
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 1.6K
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 1.6K
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 1.6K
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 1.6K
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 2.0K
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
ncbiRefSeqOther.sql 2020-04-01 12:00 1.3K
ncbiRefSeqOther.txt.gz 2020-04-01 12:00 75
ncbiRefSeqCds.sql 2020-04-01 12:00 1.4K
ncbiRefSeqCds.txt.gz 2020-04-01 12:00 181K
extNcbiRefSeq.sql 2020-04-01 12:00 1.5K
extNcbiRefSeq.txt.gz 2020-04-01 12:00 90
ncbiRefSeqPepTable.sql 2020-04-01 12:00 1.4K
ncbiRefSeqPepTable.txt.gz 2020-04-01 12:00 6.3M
seqNcbiRefSeq.sql 2020-04-01 12:00 1.6K
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 1.8K
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 1.8K
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 1.6K
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 1.8K
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 1.6K
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 1.8K
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 1.6K
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 1.8K
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 1.6K
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 1.8K
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 1.6K
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 1.8K
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
xenoRefGene.sql 2020-08-19 20:39 2.0K
xenoRefGene.txt.gz 2020-08-19 20:39 39M
xenoRefFlat.sql 2020-08-19 20:39 1.7K
xenoRefFlat.txt.gz 2020-08-19 20:39 35M
xenoRefSeqAli.sql 2020-08-19 20:39 2.1K
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
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 46K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 1.0K
tableDescriptions.sql 2024-12-28 02:12 1.5K
tableDescriptions.txt.gz 2024-12-28 02:12 7.6K
tableList.sql 2024-12-29 03:03 1.6K
tableList.txt.gz 2024-12-29 03:03 5.8K
bigFiles.sql 2024-12-29 03:03 1.4K
bigFiles.txt.gz 2024-12-29 03:03 95