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;'
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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 -
chainCanFam4Link.txt.gz 2020-07-14 04:36 1.9G
chainMonDom5Link.txt.gz 2020-07-16 19:36 1.1G
chainHg38Link.txt.gz 2018-03-16 09:56 906M
chainLoxAfr3Link.txt.gz 2020-07-15 18:23 881M
chainPanTro6Link.txt.gz 2020-07-12 11:43 873M
chainRheMac10Link.txt.gz 2020-07-12 06:49 840M
chainMm10Link.txt.gz 2018-03-16 09:23 413M
chainMm39Link.txt.gz 2020-11-25 02:00 404M
chainCanFam4.txt.gz 2020-07-14 04:16 400M
chainRBestRheMac10Link.txt.gz 2020-07-12 10:41 322M
chainRBestHg38Link.txt.gz 2018-03-16 17:58 320M
chainRBestPanTro6Link.txt.gz 2020-07-12 15:50 319M
chainSynRheMac10Link.txt.gz 2020-07-12 07:06 318M
chainSynHg38Link.txt.gz 2018-03-16 10:22 316M
chainSynPanTro6Link.txt.gz 2020-07-12 12:01 316M
chainOrnAna2Link.txt.gz 2020-07-16 15:55 314M
chainMonDom5.txt.gz 2020-07-16 19:26 306M
chainRBestLoxAfr3Link.txt.gz 2020-07-15 20:54 291M
chainSynLoxAfr3Link.txt.gz 2020-07-15 18:40 287M
chainRBestCanFam4Link.txt.gz 2020-07-14 08:30 256M
chainSynCanFam4Link.txt.gz 2020-07-14 05:04 252M
chainRBestMm10Link.txt.gz 2018-03-16 15:22 242M
chainSynMm10Link.txt.gz 2018-03-16 09:41 238M
chainHg38.txt.gz 2018-03-16 09:44 231M
chainPanTro6.txt.gz 2020-07-12 11:36 225M
chainRheMac10.txt.gz 2020-07-12 06:42 204M
chainLoxAfr3.txt.gz 2020-07-15 18:16 199M
windowmaskerSdust.txt.gz 2017-09-22 23:16 129M
rmsk.txt.gz 2017-09-22 17:55 120M
chainRBestMonDom5Link.txt.gz 2020-07-17 10:00 96M
chainSynMonDom5Link.txt.gz 2020-07-16 19:51 81M
netMm39.txt.gz 2020-11-25 02:03 63M
netMm10.txt.gz 2018-03-16 09:28 63M
netRBestLoxAfr3.txt.gz 2020-07-15 20:57 62M
netLoxAfr3.txt.gz 2020-07-15 18:25 62M
netRBestMm10.txt.gz 2018-03-16 15:29 62M
netRheMac10.txt.gz 2020-07-12 06:52 61M
netRBestRheMac10.txt.gz 2020-07-12 10:45 61M
netSynMm10.txt.gz 2018-03-16 09:42 60M
netHg38.txt.gz 2018-03-16 10:00 60M
netPanTro6.txt.gz 2020-07-12 11:46 60M
netRBestPanTro6.txt.gz 2020-07-12 15:54 60M
netRBestHg38.txt.gz 2018-03-16 18:03 60M
netSynLoxAfr3.txt.gz 2020-07-15 18:41 59M
netSynRheMac10.txt.gz 2020-07-12 07:07 57M
netSynHg38.txt.gz 2018-03-16 10:23 57M
netSynPanTro6.txt.gz 2020-07-12 12:02 57M
chainOrnAna2.txt.gz 2020-07-16 15:53 54M
netCanFam4.txt.gz 2020-07-14 04:39 51M
netRBestCanFam4.txt.gz 2020-07-14 08:33 50M
chainRBestOrnAna2Link.txt.gz 2020-07-16 17:14 49M
netSynCanFam4.txt.gz 2020-07-14 05:04 46M
chainMm10.txt.gz 2018-03-16 09:18 46M
chainMm39.txt.gz 2020-11-25 01:56 44M
xenoRefGene.txt.gz 2020-08-19 20:39 39M
xenoRefSeqAli.txt.gz 2020-08-19 20:39 38M
xenoRefFlat.txt.gz 2020-08-19 20:39 35M
chainSynOrnAna2Link.txt.gz 2020-07-16 16:06 32M
netRBestMonDom5.txt.gz 2020-07-17 10:02 29M
netMonDom5.txt.gz 2020-07-16 19:38 28M
netOrnAna2.txt.gz 2020-07-16 15:56 20M
netRBestOrnAna2.txt.gz 2020-07-16 17:16 20M
netSynMonDom5.txt.gz 2020-07-16 19:51 20M
simpleRepeat.txt.gz 2017-09-22 13:53 14M
nestedRepeats.txt.gz 2017-09-22 17:58 14M
netSynOrnAna2.txt.gz 2020-07-16 16:06 9.4M
ncbiRefSeqPepTable.txt.gz 2020-04-01 12:00 6.3M
genscan.txt.gz 2017-10-06 09:39 3.0M
chainRBestOrnAna2.txt.gz 2020-07-16 17:14 2.9M
ncbiRefSeqPsl.txt.gz 2020-04-01 11:42 2.6M
chainRBestMonDom5.txt.gz 2020-07-17 09:59 2.5M
ncbiRefSeq.txt.gz 2020-04-01 11:42 2.3M
ncbiRefSeqPredicted.txt.gz 2020-04-01 11:42 2.3M
augustusGene.txt.gz 2017-09-25 13:46 2.2M
chainRBestCanFam4.txt.gz 2020-07-14 08:28 2.0M
chainRBestLoxAfr3.txt.gz 2020-07-15 20:52 1.5M
chainRBestHg38.txt.gz 2018-03-16 17:54 1.4M
chainRBestPanTro6.txt.gz 2020-07-12 15:48 1.4M
chainRBestRheMac10.txt.gz 2020-07-12 10:39 1.4M
cpgIslandExtUnmasked.txt.gz 2017-09-22 13:49 1.1M
cpgIslandExt.txt.gz 2017-09-25 10:22 1.0M
chainRBestMm10.txt.gz 2018-03-16 15:18 916K
ncbiRefSeqLink.txt.gz 2020-04-01 11:42 848K
gold.txt.gz 2020-09-11 13:52 821K
chainSynCanFam4.txt.gz 2020-07-14 05:01 761K
gap.txt.gz 2020-09-11 13:52 499K
seqNcbiRefSeq.txt.gz 2020-04-01 12:00 453K
chainSynHg38.txt.gz 2018-03-16 10:17 446K
chainSynPanTro6.txt.gz 2020-07-12 11:58 442K
chainSynRheMac10.txt.gz 2020-07-12 07:03 437K
chainSynLoxAfr3.txt.gz 2020-07-15 18:38 436K
microsat.txt.gz 2017-09-22 20:42 260K
chainSynMonDom5.txt.gz 2020-07-16 19:51 235K
chainSynMm10.txt.gz 2018-03-16 09:37 224K
ncbiRefSeqCds.txt.gz 2020-04-01 12:00 181K
chainSynOrnAna2.txt.gz 2020-07-16 16:06 170K
chromAlias.txt.gz 2017-09-22 20:53 83K
ucscToINSDC.txt.gz 2017-09-23 01:44 66K
ucscToRefSeq.txt.gz 2017-09-23 01:44 58K
trackDb.txt.gz 2024-01-31 15:13 46K
cytoBandIdeo.txt.gz 2017-09-22 14:34 41K
chromInfo.txt.gz 2017-09-22 14:34 41K
tableDescriptions.txt.gz 2024-11-23 02:04 7.6K
tableList.txt.gz 2024-11-24 03:04 5.8K
gbLoaded.txt.gz 2020-08-19 20:54 3.9K
xenoRefSeqAli.sql 2020-08-19 20:39 2.1K
ncbiRefSeqPsl.sql 2020-04-01 11:42 2.1K
netRBestRheMac10.sql 2020-07-12 10:45 2.1K
netRBestPanTro6.sql 2020-07-12 15:54 2.1K
netRBestOrnAna2.sql 2020-07-16 17:16 2.1K
netRBestMonDom5.sql 2020-07-17 10:02 2.1K
netRBestLoxAfr3.sql 2020-07-15 20:57 2.1K
netRBestCanFam4.sql 2020-07-14 08:33 2.1K
netSynRheMac10.sql 2020-07-12 07:07 2.1K
netSynPanTro6.sql 2020-07-12 12:02 2.1K
netSynOrnAna2.sql 2020-07-16 16:06 2.1K
netSynMonDom5.sql 2020-07-16 19:51 2.1K
netSynLoxAfr3.sql 2020-07-15 18:41 2.1K
netSynCanFam4.sql 2020-07-14 05:04 2.1K
netRBestMm10.sql 2018-03-16 15:29 2.1K
netRBestHg38.sql 2018-03-16 18:03 2.1K
netRheMac10.sql 2020-07-12 06:52 2.1K
netSynMm10.sql 2018-03-16 09:42 2.1K
netSynHg38.sql 2018-03-16 10:23 2.1K
netPanTro6.sql 2020-07-12 11:46 2.1K
netOrnAna2.sql 2020-07-16 15:56 2.1K
netMonDom5.sql 2020-07-16 19:38 2.1K
netLoxAfr3.sql 2020-07-15 18:25 2.1K
netCanFam4.sql 2020-07-14 04:39 2.1K
netMm39.sql 2020-11-25 02:03 2.1K
netMm10.sql 2018-03-16 09:28 2.1K
netHg38.sql 2018-03-16 10:00 2.1K
trackDb.sql 2024-01-31 15:13 2.1K
ncbiRefSeqLink.sql 2020-04-01 11:42 2.0K
ncbiRefSeqPredicted.sql 2020-04-01 11:42 2.0K
ncbiRefSeqCurated.sql 2020-04-01 11:42 2.0K
augustusGene.sql 2017-09-25 13:46 2.0K
xenoRefGene.sql 2020-08-19 20:39 2.0K
nestedRepeats.sql 2017-09-22 17:58 2.0K
ncbiRefSeq.sql 2020-04-01 11:42 2.0K
simpleRepeat.sql 2017-09-22 13:53 1.9K
rmsk.sql 2017-09-22 17:55 1.9K
hgFindSpec.sql 2024-01-31 15:13 1.8K
chainRBestRheMac10.sql 2020-07-12 10:39 1.8K
chainRBestPanTro6.sql 2020-07-12 15:48 1.8K
chainRBestOrnAna2.sql 2020-07-16 17:14 1.8K
chainRBestMonDom5.sql 2020-07-17 09:59 1.8K
chainRBestLoxAfr3.sql 2020-07-15 20:52 1.8K
chainRBestCanFam4.sql 2020-07-14 08:28 1.8K
chainSynRheMac10.sql 2020-07-12 07:03 1.8K
xenoRefFlat.sql 2020-08-19 20:39 1.7K
chainSynPanTro6.sql 2020-07-12 11:58 1.7K
chainSynOrnAna2.sql 2020-07-16 16:06 1.7K
chainSynMonDom5.sql 2020-07-16 19:51 1.7K
chainSynLoxAfr3.sql 2020-07-15 18:38 1.7K
chainSynCanFam4.sql 2020-07-14 05:01 1.7K
chainRBestMm10.sql 2018-03-16 15:18 1.7K
chainRBestHg38.sql 2018-03-16 17:54 1.7K
chainRheMac10.sql 2020-07-12 06:42 1.7K
cpgIslandExtUnmasked.sql 2017-09-22 13:49 1.7K
chainSynMm10.sql 2018-03-16 09:37 1.7K
chainSynHg38.sql 2018-03-16 10:17 1.7K
chainPanTro6.sql 2020-07-12 11:36 1.7K
chainOrnAna2.sql 2020-07-16 15:53 1.7K
chainMonDom5.sql 2020-07-16 19:26 1.7K
chainLoxAfr3.sql 2020-07-15 18:16 1.7K
chainCanFam4.sql 2020-07-14 04:16 1.7K
chainMm39.sql 2020-11-25 01:56 1.7K
chainMm10.sql 2018-03-16 09:18 1.7K
chainHg38.sql 2018-03-16 09:44 1.7K
cpgIslandExt.sql 2017-09-25 10:22 1.7K
genscan.sql 2017-10-06 09:39 1.7K
gold.sql 2020-09-11 13:52 1.7K
history.txt.gz 2020-09-11 16:38 1.7K
gap.sql 2020-09-11 13:52 1.6K
gbLoaded.sql 2020-08-19 20:54 1.6K
history.sql 2020-09-11 16:38 1.6K
chainRBestRheMac10Link.sql 2020-07-12 10:41 1.6K
chainRBestPanTro6Link.sql 2020-07-12 15:50 1.6K
chainRBestOrnAna2Link.sql 2020-07-16 17:14 1.6K
chainRBestMonDom5Link.sql 2020-07-17 10:00 1.6K
chainRBestLoxAfr3Link.sql 2020-07-15 20:54 1.6K
chainRBestCanFam4Link.sql 2020-07-14 08:30 1.6K
chainSynRheMac10Link.sql 2020-07-12 07:06 1.6K
chainSynPanTro6Link.sql 2020-07-12 12:01 1.6K
chainSynOrnAna2Link.sql 2020-07-16 16:06 1.6K
chainSynMonDom5Link.sql 2020-07-16 19:51 1.6K
chainSynLoxAfr3Link.sql 2020-07-15 18:40 1.6K
chainSynCanFam4Link.sql 2020-07-14 05:04 1.6K
chainRBestMm10Link.sql 2018-03-16 15:22 1.6K
chainRBestHg38Link.sql 2018-03-16 17:58 1.6K
chainRheMac10Link.sql 2020-07-12 06:49 1.6K
chainSynMm10Link.sql 2018-03-16 09:41 1.6K
chainSynHg38Link.sql 2018-03-16 10:22 1.6K
chainPanTro6Link.sql 2020-07-12 11:43 1.6K
chainOrnAna2Link.sql 2020-07-16 15:55 1.6K
chainMonDom5Link.sql 2020-07-16 19:36 1.6K
chainLoxAfr3Link.sql 2020-07-15 18:23 1.6K
chainCanFam4Link.sql 2020-07-14 04:36 1.6K
seqNcbiRefSeq.sql 2020-04-01 12:00 1.6K
tableList.sql 2024-11-24 03:04 1.6K
chainMm39Link.sql 2020-11-25 02:00 1.6K
chainMm10Link.sql 2018-03-16 09:23 1.6K
chainHg38Link.sql 2018-03-16 09:56 1.6K
cytoBandIdeo.sql 2017-09-22 14:34 1.5K
windowmaskerSdust.sql 2017-09-22 23:16 1.5K
microsat.sql 2017-09-22 20:42 1.5K
extNcbiRefSeq.sql 2020-04-01 12:00 1.5K
ucscToRefSeq.sql 2017-09-23 01:44 1.5K
ucscToINSDC.sql 2017-09-23 01:44 1.4K
chromAlias.sql 2017-09-22 20:53 1.4K
tableDescriptions.sql 2024-11-23 02:04 1.4K
chromInfo.sql 2017-09-22 14:34 1.4K
ncbiRefSeqPepTable.sql 2020-04-01 12:00 1.4K
bigFiles.sql 2024-11-24 03:04 1.4K
grp.sql 2017-09-22 14:34 1.4K
ncbiRefSeqCds.sql 2020-04-01 12:00 1.4K
ncbiRefSeqOther.sql 2020-04-01 12:00 1.3K
gc5BaseBw.sql 2017-09-22 14:34 1.3K
hgFindSpec.txt.gz 2024-01-31 15:13 1.0K
ncbiRefSeqCurated.txt.gz 2020-04-01 11:42 328
grp.txt.gz 2017-09-22 14:34 213
bigFiles.txt.gz 2024-11-24 03:04 95
extNcbiRefSeq.txt.gz 2020-04-01 12:00 90
ncbiRefSeqOther.txt.gz 2020-04-01 12:00 75
gc5BaseBw.txt.gz 2017-09-22 14:34 66