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:
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
loxAfr3.agp.gz - Description of how the assembly was generated from
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
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
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
loxAfr3.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 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
Or with wget, all files:
With wget, a single file:
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80