This directory contains the Jul. 2011 (HetGla_1.0/hetGla1) assembly of the naked mole-rat genome
(hetGla1, HetGla_1.0 (NCBI project 68323, accession GCA_000230455.1)), as well as repeat annotations and GenBank sequences.
This assembly was produced by the National Center for Biotechnology Information (NCBI).
For more information on the naked mole-rat genome, see the project website:
Files included in this directory:
hetGla1.2bit - contains the complete naked mole-rat/hetGla1 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
hetGla1.agp.gz - Description of how the assembly was generated from
hetGla1.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.
hetGla1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
hetGla1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. RepeatMasker version: April 26 2011 (open-3-3-0) (open-3-2-9)
RepeatMasker library version: 0110920
hetGla1.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 - Naked mole-rat 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
hetGla1.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/hetGla1/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/hetGla1/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