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 -
xenoRefSeqAli.txt.gz 2020-08-19 20:39 38M
xenoRefSeqAli.sql 2020-08-19 20:39 2.1K
xenoRefGene.txt.gz 2020-08-19 20:39 39M
xenoRefGene.sql 2020-08-19 20:39 2.0K
xenoRefFlat.txt.gz 2020-08-19 20:39 35M
xenoRefFlat.sql 2020-08-19 20:39 1.7K
windowmaskerSdust.txt.gz 2017-09-22 23:16 129M
windowmaskerSdust.sql 2017-09-22 23:16 1.5K
ucscToRefSeq.txt.gz 2017-09-23 01:44 58K
ucscToRefSeq.sql 2017-09-23 01:44 1.5K
ucscToINSDC.txt.gz 2017-09-23 01:44 66K
ucscToINSDC.sql 2017-09-23 01:44 1.4K
trackDb_pushedout.txt.gz 2023-12-05 13:52 32K
trackDb_pushedout.sql 2023-12-05 13:52 2.1K
trackDb.txt.gz 2024-01-31 15:13 46K
trackDb.sql 2024-01-31 15:13 2.1K
tableList.txt.gz 2024-04-14 03:05 6.0K
tableList.sql 2024-04-14 03:05 1.6K
tableDescriptions.txt.gz 2024-04-13 02:04 7.6K
tableDescriptions.sql 2024-04-13 02:04 1.5K
simpleRepeat.txt.gz 2017-09-22 13:53 14M
simpleRepeat.sql 2017-09-22 13:53 1.9K
seqNcbiRefSeq.txt.gz 2020-04-01 12:00 453K
seqNcbiRefSeq.sql 2020-04-01 12:00 1.6K
rmsk.txt.gz 2017-09-22 17:55 120M
rmsk.sql 2017-09-22 17:55 1.9K
netSynRheMac10.txt.gz 2020-07-12 07:07 57M
netSynRheMac10.sql 2020-07-12 07:07 2.1K
netSynPanTro6.txt.gz 2020-07-12 12:02 57M
netSynPanTro6.sql 2020-07-12 12:02 2.1K
netSynOrnAna2.txt.gz 2020-07-16 16:06 9.4M
netSynOrnAna2.sql 2020-07-16 16:06 2.1K
netSynMonDom5.txt.gz 2020-07-16 19:51 20M
netSynMonDom5.sql 2020-07-16 19:51 2.1K
netSynMm10.txt.gz 2018-03-16 09:42 60M
netSynMm10.sql 2018-03-16 09:42 2.1K
netSynLoxAfr3.txt.gz 2020-07-15 18:41 59M
netSynLoxAfr3.sql 2020-07-15 18:41 2.1K
netSynHg38.txt.gz 2018-03-16 10:23 57M
netSynHg38.sql 2018-03-16 10:23 2.1K
netSynCanFam4.txt.gz 2020-07-14 05:04 46M
netSynCanFam4.sql 2020-07-14 05:04 2.1K
netRheMac10.txt.gz 2020-07-12 06:52 61M
netRheMac10.sql 2020-07-12 06:52 2.1K
netRBestRheMac10.txt.gz 2020-07-12 10:45 61M
netRBestRheMac10.sql 2020-07-12 10:45 2.1K
netRBestPanTro6.txt.gz 2020-07-12 15:54 60M
netRBestPanTro6.sql 2020-07-12 15:54 2.1K
netRBestOrnAna2.txt.gz 2020-07-16 17:16 20M
netRBestOrnAna2.sql 2020-07-16 17:16 2.1K
netRBestMonDom5.txt.gz 2020-07-17 10:02 29M
netRBestMonDom5.sql 2020-07-17 10:02 2.1K
netRBestMm10.txt.gz 2018-03-16 15:29 62M
netRBestMm10.sql 2018-03-16 15:29 2.1K
netRBestLoxAfr3.txt.gz 2020-07-15 20:57 62M
netRBestLoxAfr3.sql 2020-07-15 20:57 2.1K
netRBestHg38.txt.gz 2018-03-16 18:03 60M
netRBestHg38.sql 2018-03-16 18:03 2.1K
netRBestCanFam4.txt.gz 2020-07-14 08:33 50M
netRBestCanFam4.sql 2020-07-14 08:33 2.1K
netPanTro6.txt.gz 2020-07-12 11:46 60M
netPanTro6.sql 2020-07-12 11:46 2.1K
netOrnAna2.txt.gz 2020-07-16 15:56 20M
netOrnAna2.sql 2020-07-16 15:56 2.1K
netMonDom5.txt.gz 2020-07-16 19:38 28M
netMonDom5.sql 2020-07-16 19:38 2.1K
netMm39.txt.gz 2020-11-25 02:03 63M
netMm39.sql 2020-11-25 02:03 2.1K
netMm10.txt.gz 2018-03-16 09:28 63M
netMm10.sql 2018-03-16 09:28 2.1K
netLoxAfr3.txt.gz 2020-07-15 18:25 62M
netLoxAfr3.sql 2020-07-15 18:25 2.1K
netHg38.txt.gz 2018-03-16 10:00 60M
netHg38.sql 2018-03-16 10:00 2.1K
netCanFam4.txt.gz 2020-07-14 04:39 51M
netCanFam4.sql 2020-07-14 04:39 2.1K
nestedRepeats.txt.gz 2017-09-22 17:58 14M
nestedRepeats.sql 2017-09-22 17:58 2.0K
ncbiRefSeqPsl.txt.gz 2020-04-01 11:42 2.6M
ncbiRefSeqPsl.sql 2020-04-01 11:42 2.1K
ncbiRefSeqPredicted.txt.gz 2020-04-01 11:42 2.3M
ncbiRefSeqPredicted.sql 2020-04-01 11:42 2.0K
ncbiRefSeqPepTable.txt.gz 2020-04-01 12:00 6.3M
ncbiRefSeqPepTable.sql 2020-04-01 12:00 1.4K
ncbiRefSeqOther.txt.gz 2020-04-01 12:00 75
ncbiRefSeqOther.sql 2020-04-01 12:00 1.3K
ncbiRefSeqLink.txt.gz 2020-04-01 11:42 848K
ncbiRefSeqLink.sql 2020-04-01 11:42 2.0K
ncbiRefSeqCurated.txt.gz 2020-04-01 11:42 328
ncbiRefSeqCurated.sql 2020-04-01 11:42 2.0K
ncbiRefSeqCds.txt.gz 2020-04-01 12:00 181K
ncbiRefSeqCds.sql 2020-04-01 12:00 1.4K
ncbiRefSeq.txt.gz 2020-04-01 11:42 2.3M
ncbiRefSeq.sql 2020-04-01 11:42 2.0K
microsat.txt.gz 2017-09-22 20:42 260K
microsat.sql 2017-09-22 20:42 1.5K
history.txt.gz 2020-09-11 16:38 1.7K
history.sql 2020-09-11 16:38 1.6K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.0K
hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 1.0K
hgFindSpec.sql 2024-01-31 15:13 1.8K
grp.txt.gz 2017-09-22 14:34 213
grp.sql 2017-09-22 14:34 1.4K
gold.txt.gz 2020-09-11 13:52 821K
gold.sql 2020-09-11 13:52 1.7K
genscan.txt.gz 2017-10-06 09:39 3.0M
genscan.sql 2017-10-06 09:39 1.7K
gc5BaseBw.txt.gz 2017-09-22 14:34 66
gc5BaseBw.sql 2017-09-22 14:34 1.3K
gbLoaded.txt.gz 2020-08-19 20:54 3.9K
gbLoaded.sql 2020-08-19 20:54 1.6K
gap.txt.gz 2020-09-11 13:52 499K
gap.sql 2020-09-11 13:52 1.6K
extNcbiRefSeq.txt.gz 2020-04-01 12:00 90
extNcbiRefSeq.sql 2020-04-01 12:00 1.5K
cytoBandIdeo.txt.gz 2017-09-22 14:34 41K
cytoBandIdeo.sql 2017-09-22 14:34 1.5K
cpgIslandExtUnmasked.txt.gz 2017-09-22 13:49 1.1M
cpgIslandExtUnmasked.sql 2017-09-22 13:49 1.7K
cpgIslandExt.txt.gz 2017-09-25 10:22 1.0M
cpgIslandExt.sql 2017-09-25 10:22 1.7K
chromInfo.txt.gz 2017-09-22 14:34 41K
chromInfo.sql 2017-09-22 14:34 1.4K
chromAlias.txt.gz 2017-09-22 20:53 83K
chromAlias.sql 2017-09-22 20:53 1.4K
chainSynRheMac10Link.txt.gz 2020-07-12 07:06 318M
chainSynRheMac10Link.sql 2020-07-12 07:06 1.6K
chainSynRheMac10.txt.gz 2020-07-12 07:03 437K
chainSynRheMac10.sql 2020-07-12 07:03 1.8K
chainSynPanTro6Link.txt.gz 2020-07-12 12:01 316M
chainSynPanTro6Link.sql 2020-07-12 12:01 1.6K
chainSynPanTro6.txt.gz 2020-07-12 11:58 442K
chainSynPanTro6.sql 2020-07-12 11:58 1.7K
chainSynOrnAna2Link.txt.gz 2020-07-16 16:06 32M
chainSynOrnAna2Link.sql 2020-07-16 16:06 1.6K
chainSynOrnAna2.txt.gz 2020-07-16 16:06 170K
chainSynOrnAna2.sql 2020-07-16 16:06 1.7K
chainSynMonDom5Link.txt.gz 2020-07-16 19:51 81M
chainSynMonDom5Link.sql 2020-07-16 19:51 1.6K
chainSynMonDom5.txt.gz 2020-07-16 19:51 235K
chainSynMonDom5.sql 2020-07-16 19:51 1.7K
chainSynMm10Link.txt.gz 2018-03-16 09:41 238M
chainSynMm10Link.sql 2018-03-16 09:41 1.6K
chainSynMm10.txt.gz 2018-03-16 09:37 224K
chainSynMm10.sql 2018-03-16 09:37 1.7K
chainSynLoxAfr3Link.txt.gz 2020-07-15 18:40 287M
chainSynLoxAfr3Link.sql 2020-07-15 18:40 1.6K
chainSynLoxAfr3.txt.gz 2020-07-15 18:38 436K
chainSynLoxAfr3.sql 2020-07-15 18:38 1.7K
chainSynHg38Link.txt.gz 2018-03-16 10:22 316M
chainSynHg38Link.sql 2018-03-16 10:22 1.6K
chainSynHg38.txt.gz 2018-03-16 10:17 446K
chainSynHg38.sql 2018-03-16 10:17 1.7K
chainSynCanFam4Link.txt.gz 2020-07-14 05:04 252M
chainSynCanFam4Link.sql 2020-07-14 05:04 1.6K
chainSynCanFam4.txt.gz 2020-07-14 05:01 761K
chainSynCanFam4.sql 2020-07-14 05:01 1.7K
chainRheMac10Link.txt.gz 2020-07-12 06:49 840M
chainRheMac10Link.sql 2020-07-12 06:49 1.6K
chainRheMac10.txt.gz 2020-07-12 06:42 204M
chainRheMac10.sql 2020-07-12 06:42 1.7K
chainRBestRheMac10Link.txt.gz 2020-07-12 10:41 322M
chainRBestRheMac10Link.sql 2020-07-12 10:41 1.6K
chainRBestRheMac10.txt.gz 2020-07-12 10:39 1.4M
chainRBestRheMac10.sql 2020-07-12 10:39 1.8K
chainRBestPanTro6Link.txt.gz 2020-07-12 15:50 319M
chainRBestPanTro6Link.sql 2020-07-12 15:50 1.6K
chainRBestPanTro6.txt.gz 2020-07-12 15:48 1.4M
chainRBestPanTro6.sql 2020-07-12 15:48 1.8K
chainRBestOrnAna2Link.txt.gz 2020-07-16 17:14 49M
chainRBestOrnAna2Link.sql 2020-07-16 17:14 1.6K
chainRBestOrnAna2.txt.gz 2020-07-16 17:14 2.9M
chainRBestOrnAna2.sql 2020-07-16 17:14 1.8K
chainRBestMonDom5Link.txt.gz 2020-07-17 10:00 96M
chainRBestMonDom5Link.sql 2020-07-17 10:00 1.6K
chainRBestMonDom5.txt.gz 2020-07-17 09:59 2.5M
chainRBestMonDom5.sql 2020-07-17 09:59 1.8K
chainRBestMm10Link.txt.gz 2018-03-16 15:22 242M
chainRBestMm10Link.sql 2018-03-16 15:22 1.6K
chainRBestMm10.txt.gz 2018-03-16 15:18 916K
chainRBestMm10.sql 2018-03-16 15:18 1.7K
chainRBestLoxAfr3Link.txt.gz 2020-07-15 20:54 291M
chainRBestLoxAfr3Link.sql 2020-07-15 20:54 1.6K
chainRBestLoxAfr3.txt.gz 2020-07-15 20:52 1.5M
chainRBestLoxAfr3.sql 2020-07-15 20:52 1.8K
chainRBestHg38Link.txt.gz 2018-03-16 17:58 320M
chainRBestHg38Link.sql 2018-03-16 17:58 1.6K
chainRBestHg38.txt.gz 2018-03-16 17:54 1.4M
chainRBestHg38.sql 2018-03-16 17:54 1.7K
chainRBestCanFam4Link.txt.gz 2020-07-14 08:30 256M
chainRBestCanFam4Link.sql 2020-07-14 08:30 1.6K
chainRBestCanFam4.txt.gz 2020-07-14 08:28 2.0M
chainRBestCanFam4.sql 2020-07-14 08:28 1.8K
chainPanTro6Link.txt.gz 2020-07-12 11:43 873M
chainPanTro6Link.sql 2020-07-12 11:43 1.6K
chainPanTro6.txt.gz 2020-07-12 11:36 225M
chainPanTro6.sql 2020-07-12 11:36 1.7K
chainOrnAna2Link.txt.gz 2020-07-16 15:55 314M
chainOrnAna2Link.sql 2020-07-16 15:55 1.6K
chainOrnAna2.txt.gz 2020-07-16 15:53 54M
chainOrnAna2.sql 2020-07-16 15:53 1.7K
chainMonDom5Link.txt.gz 2020-07-16 19:36 1.1G
chainMonDom5Link.sql 2020-07-16 19:36 1.6K
chainMonDom5.txt.gz 2020-07-16 19:26 306M
chainMonDom5.sql 2020-07-16 19:26 1.7K
chainMm39Link.txt.gz 2020-11-25 02:00 404M
chainMm39Link.sql 2020-11-25 02:00 1.6K
chainMm39.txt.gz 2020-11-25 01:56 44M
chainMm39.sql 2020-11-25 01:56 1.7K
chainMm10Link.txt.gz 2018-03-16 09:23 413M
chainMm10Link.sql 2018-03-16 09:23 1.6K
chainMm10.txt.gz 2018-03-16 09:18 46M
chainMm10.sql 2018-03-16 09:18 1.7K
chainLoxAfr3Link.txt.gz 2020-07-15 18:23 881M
chainLoxAfr3Link.sql 2020-07-15 18:23 1.6K
chainLoxAfr3.txt.gz 2020-07-15 18:16 199M
chainLoxAfr3.sql 2020-07-15 18:16 1.7K
chainHg38Link.txt.gz 2018-03-16 09:56 906M
chainHg38Link.sql 2018-03-16 09:56 1.6K
chainHg38.txt.gz 2018-03-16 09:44 231M
chainHg38.sql 2018-03-16 09:44 1.7K
chainCanFam4Link.txt.gz 2020-07-14 04:36 1.9G
chainCanFam4Link.sql 2020-07-14 04:36 1.6K
chainCanFam4.txt.gz 2020-07-14 04:16 400M
chainCanFam4.sql 2020-07-14 04:16 1.7K
bigFiles.txt.gz 2024-04-14 03:05 95
bigFiles.sql 2024-04-14 03:05 1.4K
augustusGene.txt.gz 2017-09-25 13:46 2.2M
augustusGene.sql 2017-09-25 13:46 2.0K