This directory contains the Feb. 2007 assembly of the lizard genome
(anoCar1, Broad Institute AnoCar (1.0)), 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 lizard genome, see the project website:
http://www.broad.mit.edu/tools/data/data-vert.html
Files included in this directory:
anoCar1.2bit - contains the complete lizard/anoCar1 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
anoCar1.agp.gz - Description of how the assembly was generated from
fragments.
anoCar1.fa.gz - "Soft-masked" assembly sequence in one file.
Repeats from WindowMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case. Note, this sequence is *not* masked with
the RepeatMasker .out specification.
anoCar1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
anoCar1.WMSdust.bed.gz - Repeat areas identified by WindowMasker with
the -sdust option.
anoCar1.fa.out.gz - RepeatMasker .out file.
RepeatMasker was run with the -s (sensitive) setting.
RepeatMasker version: October 6, 2006 (open-3-1-6)
with RepBase libraries: RepBase Update 20061006.
anoCar1.qual.qv.gz - base by base qual scores for anoCar1 assembly.
Values vary from 0 to 60.
anoCar1.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.
anoCar1.quals.fa.gz - quality scores in fasta file format
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Lizard 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.
anoCar1.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, then
go to the directory goldenPath/anoCar1/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 -
anoCar1.2bit 2007-02-17 09:15 489M
anoCar1.WMSdust.bed.gz 2007-02-16 16:57 54M
anoCar1.agp.gz 2007-03-21 14:13 1.2M
anoCar1.chrom.sizes 2007-02-16 11:25 139K
anoCar1.fa.gz 2007-03-21 14:22 555M
anoCar1.fa.masked.gz 2007-03-21 14:28 349M
anoCar1.fa.out.gz 2007-03-21 14:13 22M
anoCar1.qual.qv.gz 2007-02-13 19:13 154M
anoCar1.quals.fa.gz 2009-06-09 10:41 157M
anoCar1.trf.bed.gz 2007-03-21 14:13 5.5M
genes/ 2020-02-05 13:46 -
md5sum.txt 2014-01-03 16:11 562
mrna.fa.gz 2019-10-16 17:40 48K
mrna.fa.gz.md5 2019-10-16 17:40 45
upstream1000.fa.gz 2019-10-16 17:40 646K
upstream1000.fa.gz.md5 2019-10-16 17:40 53
upstream2000.fa.gz 2019-10-16 17:40 1.2M
upstream2000.fa.gz.md5 2019-10-16 17:40 53
upstream5000.fa.gz 2019-10-16 17:41 2.9M
upstream5000.fa.gz.md5 2019-10-16 17:41 53
xenoMrna.fa.gz 2016-03-22 07:57 5.0G
xenoMrna.fa.gz.md5 2016-03-22 07:57 49
xenoRefMrna.fa.gz 2019-10-16 17:40 331M
xenoRefMrna.fa.gz.md5 2019-10-16 17:40 52