This directory contains the May 2012 (OchPri3.0/ochPri3) assembly of the
pika genome (ochPri3, Broad Institute),
as well as repeat annotations and GenBank sequences.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/771
http://www.ncbi.nlm.nih.gov/genome/assembly/681538
http://www.ncbi.nlm.nih.gov/bioproject/193497
Files included in this directory:
ochPri3.2bit - contains the complete pika/ochPri3 genome sequence
in the 2bit file format. Repeats from RepeatMasker and Tandem Repeats
Finder (with period of 12 or less) are shown in lower case; non-repeating
sequence is shown in upper case. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
ochPri3.agp.gz - Description of how the assembly was generated from
fragments.
ochPri3.fa.gz - "Soft-masked" assembly sequence in one file.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
ochPri3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
ochPri3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
June 20 2013 (open-4-0-3) version of RepeatMasker
RepBase library: RELEASE 20130422
ochPri3.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Pika mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
ochPri3.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
ochPri3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
ochPri3.gc5Base.wig.gz - wiggle database table for the GC Percent track
- this is an older standard alternative to the current
- bigWig format of the track, sometimes usefull for analysis
ochPri3.gc5Base.wib - binary data to correspond with the gc5Base.wig file
see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html
and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
for a discussion of how to use the wig.gz and .wib files for
interaction with the GC percent data values
ochPri3.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
------------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/ochPri3/bigZips. 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.cse.ucsc.edu/goldenPath/ochPri3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ochPri3/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ochPri3/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ochPri3/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
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The Pika sequence is made freely available before scientific publication
with the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing particular
genes and regions if the provider of these data (The Broad Institute) is
properly acknowledged.
3. The center producing the data reserves the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice. 1. The data may
be freely downloaded, used in analyses, and repackaged in databases.
-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
genes/ 2020-04-27 14:08 -
md5sum.txt 2019-01-17 15:56 479
mrna.fa.gz 2019-10-16 12:18 1.2K
mrna.fa.gz.md5 2019-10-16 12:18 45
ochPri3.2bit 2013-06-20 15:16 552M
ochPri3.agp.gz 2014-04-23 14:16 3.3M
ochPri3.chrom.sizes 2013-06-18 15:02 175K
ochPri3.chromAlias.bb 2022-09-08 14:14 2.3M
ochPri3.chromAlias.txt 2022-09-08 14:14 418K
ochPri3.fa.gz 2014-04-23 14:28 618M
ochPri3.fa.masked.gz 2014-04-23 14:37 441M
ochPri3.fa.out.gz 2014-04-23 14:17 85M
ochPri3.gc5Base.wib 2019-01-17 14:50 382M
ochPri3.gc5Base.wig.gz 2019-01-17 14:50 8.6M
ochPri3.gc5Base.wigVarStep.gz 2013-06-18 15:12 1.0G
ochPri3.trf.bed.gz 2014-04-23 14:17 3.5M
xenoRefMrna.fa.gz 2019-10-16 12:18 331M
xenoRefMrna.fa.gz.md5 2019-10-16 12:18 52