This directory contains the May 2005 assembly of the elephant genome
(loxAfr1) obtained from the Broad Institute. More information may be
found http://www.broad.mit.edu/mammals/.
Files included in this directory:
assembly.agp.gz - Description of how the assembly was generated from
fragments.
md5sum.txt - MD5 checksum of these files to verify correct transmission.
rmsk.out.gz - RepeatMasker .out file for scaffolds. These were created
by RepeatMasker at the -s sensitive setting.
scaffold.fa.gz - unmasked scaffolds sequences obtained from the Broad
Institute.
scaffoldSoftMask.fa.gz - The assembly sequence in one file per chromosome.
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. RepeatMasker May 3 2005 (open-3-1-0) version with RepBase
libraries: RepBase Update 9.11, RM database version 20050112.
trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into one
.bed file for all the scaffolds.
loxAfr1.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 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/loxAfr1/bigZips. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Name Last modified Size Description
Parent Directory -
md5sum.txt 2007-10-26 12:34 247
trf.bed.gz 2005-05-23 12:43 1.2M
loxAfr1.chrom.sizes 2005-05-23 13:06 4.6M
assembly.agp.gz 2005-05-20 20:08 18M
rmsk.out.gz 2005-05-23 11:45 103M
scaffold.fa.gz 2005-05-22 15:18 715M
scaffoldSoftMask.fa.gz 2005-05-23 12:52 760M