This directory contains the April 2005 Spur_0.5 release of the
S. purpuratus genome (strPur1) obtained from the Baylor College of
Medicine Human Genome Sequencing Center.
Files included in this directory:
strPur1.2bit - contains the complete S. purpuratus/strPur1 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
allAgp.tar.gz - Description of how the assembly was generated from
fragments.
allFa.tar.gz- Sequences downloaded from Baylor 19 April 2005.
allFaMasked.tar.gz - The assembly sequence with repeats
masked by capital Ns; non-repeating sequence is shown in upper case.
allOut.tar.gz - RepeatMasker .out file for chromosomes. These were created
by RepeatMasker at the -s sensitive setting.
allTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into one
.bed file per chromosomes.
md5sum.txt - Checksum file.
mrna.fa.gz - S. purpuratus mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
strPur1.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
-----------------------------------------------------------------
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.cse.ucsc.edu, then go to
the directory goldenPath/strPur1/bigZips. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
These data are made 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 providers of these data are properly acknowledged.
Please cite the BCM-HGSC web site or publications from BCM-HGSC referring to
the genome sequence.
3. BCM HGSC plans to publish the assembly and genomic annotation of the dataset,
including large-scale identification of regions of evolutionary conservation.
4. This is in accordance with, and with the understandings in the Fort
Lauderdale meeting discussing Community Resource Projects and the resulting
NHGRI policy statement.
5. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory -
strPur1.chrom.sizes 2005-04-19 02:47 8.2M
strPur1.2bit 2005-07-16 02:18 274M
allAgp.tar.gz 2006-02-22 12:07 5.2M
allFa.tar.gz 2006-02-22 12:41 494M
allFaMasked.tar.gz 2006-02-22 12:56 246M
allTrf.tar.gz 2006-02-22 12:56 4.0M
allOut.tar.gz 2006-02-22 16:43 19M
md5sum.txt 2013-12-10 14:49 336
xenoMrna.fa.gz 2016-02-27 12:11 4.9G
xenoMrna.fa.gz.md5 2016-02-27 12:12 49
mrna.fa.gz 2019-10-17 21:17 28M
mrna.fa.gz.md5 2019-10-17 21:17 45
xenoRefMrna.fa.gz 2019-10-17 21:18 330M
xenoRefMrna.fa.gz.md5 2019-10-17 21:18 52
refMrna.fa.gz 2019-10-17 21:18 380K
refMrna.fa.gz.md5 2019-10-17 21:18 48
strPur1.fa.gz 2020-01-23 02:26 254M