This directory contains the Jul. 2009 assembly of the elephant genome
(loxAfr3, Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000)),
as well as repeat annotations and GenBank sequences.
This assembly was produced by the Broad Institute.
For more information on the elephant genome, see the project website:
http://www.broadinstitute.org/science/projects/mammals-models/elephant/elephant
Files included in this directory:
loxAfr3.2bit - contains the complete elephant/loxAfr3 genome sequence
in the 2bit file format. 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/cvs.html
http://genome.ucsc.edu/admin/jk-install.html
loxAfr3.agp.gz - Description of how the assembly was generated from
fragments.
loxAfr3.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.
loxAfr3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
loxAfr3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. RM version: June 4 2009 (open-3-2-8)
repeat library version: RELEASE 20090604
loxAfr3.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 - Elephant 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.
loxAfr3.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
loxAfr3.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
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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/loxAfr3/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/loxAfr3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/loxAfr3/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/loxAfr3/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/loxAfr3/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
Name Last modified Size Description
Parent Directory -
genes/ 2020-10-02 13:38 -
upstream1000.fa.gz 2019-10-16 10:42 20
upstream2000.fa.gz 2019-10-16 10:42 20
upstream5000.fa.gz 2019-10-16 10:42 20
mrna.fa.gz.md5 2019-10-16 10:30 45
refMrna.fa.gz.md5 2019-10-16 10:42 48
xenoMrna.fa.gz.md5 2019-10-16 10:41 49
xenoRefMrna.fa.gz.md5 2019-10-16 10:42 52
upstream1000.fa.gz.md5 2019-10-16 10:42 53
upstream2000.fa.gz.md5 2019-10-16 10:42 53
upstream5000.fa.gz.md5 2019-10-16 10:42 53
md5sum.txt 2009-07-29 12:00 304
mrna.fa.gz 2019-10-16 10:30 10K
refMrna.fa.gz 2019-10-16 10:42 13K
loxAfr3.chrom.sizes 2009-07-15 09:54 44K
loxAfr3.chromAlias.txt 2022-09-08 14:13 94K
loxAfr3.chromAlias.bb 2022-09-08 14:13 599K
loxAfr3.trf.bed.gz 2009-07-29 11:06 1.9M
loxAfr3.agp.gz 2009-07-29 11:04 2.5M
loxAfr3.fa.out.gz 2009-07-29 11:06 172M
xenoRefMrna.fa.gz 2019-10-16 10:42 331M
loxAfr3.fa.masked.gz 2009-07-29 11:47 545M
loxAfr3.2bit 2009-07-16 11:08 800M
loxAfr3.fa.gz 2009-07-29 11:23 1.0G
xenoMrna.fa.gz 2019-10-16 10:41 6.8G