This directory contains the Sept. 2008 assembly of the sea hare genome
(aplCal1, Broad Institute v. Aplcal2.0), as well as repeat annotations and GenBank sequences.
This assembly was produced by the Broad Institute at MIT and Harvard.
For more information on the sea hare genome, see the project website:
http://www.broad.mit.edu/node/435
Files included in this directory:
aplCal1.2bit - contains the complete sea hare/aplCal1 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
aplCal1.agp.gz - Description of how the assembly was generated from
fragments.
aplCal1.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.
aplCal1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
aplCal1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
(Jan 29 2009 open-3-2-7 version of RepeatMasker - LIB version RepeatMasker090129)
aplCal1.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.
est.fa.gz - Sea Hare ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Sea Hare mRNA from GenBank. 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.
aplCal1.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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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/aplCal1/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/aplCal1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/aplCal1/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/aplCal1/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/aplCal1/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
The Sea Hare 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.
Name Last modified Size Description
Parent Directory -
aplCal1.chrom.sizes 2009-05-11 20:53 169K
aplCal1.2bit 2009-05-13 17:15 176M
aplCal1.agp.gz 2009-05-28 10:39 1.5M
aplCal1.fa.out.gz 2009-05-28 10:39 16M
aplCal1.trf.bed.gz 2009-05-28 10:39 8.1M
aplCal1.fa.gz 2009-05-28 10:43 186M
aplCal1.fa.masked.gz 2009-05-28 10:46 173M
refMrna.fa.gz 2010-01-13 16:47 20
refMrna.fa.gz.md5 2010-01-13 16:47 48
xenoMrna.fa.gz 2012-10-12 11:04 3.2G
xenoMrna.fa.gz.md5 2012-10-12 11:07 49
md5sum.txt 2013-12-11 10:20 304
mrna.fa.gz 2019-10-14 20:51 345K
mrna.fa.gz.md5 2019-10-14 20:51 45
est.fa.gz 2019-10-14 20:56 51M
est.fa.gz.md5 2019-10-14 20:56 44
xenoRefMrna.fa.gz 2019-10-14 20:56 331M
xenoRefMrna.fa.gz.md5 2019-10-14 20:56 52