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 - xenoRefMrna.fa.gz.md5 2019-10-16 17:40 52 xenoRefMrna.fa.gz 2019-10-16 17:40 331M xenoMrna.fa.gz.md5 2016-03-22 07:57 49 xenoMrna.fa.gz 2016-03-22 07:57 5.0G upstream5000.fa.gz.md5 2019-10-16 17:41 53 upstream5000.fa.gz 2019-10-16 17:41 2.9M upstream2000.fa.gz.md5 2019-10-16 17:40 53 upstream2000.fa.gz 2019-10-16 17:40 1.2M upstream1000.fa.gz.md5 2019-10-16 17:40 53 upstream1000.fa.gz 2019-10-16 17:40 646K mrna.fa.gz.md5 2019-10-16 17:40 45 mrna.fa.gz 2019-10-16 17:40 48K md5sum.txt 2014-01-03 16:11 562 genes/ 2020-02-05 13:46 - anoCar1.trf.bed.gz 2007-03-21 14:13 5.5M anoCar1.qual.qv.gz 2007-02-13 19:13 154M anoCar1.fa.out.gz 2007-03-21 14:13 22M anoCar1.fa.masked.gz 2007-03-21 14:28 349M anoCar1.fa.gz 2007-03-21 14:22 555M anoCar1.chrom.sizes 2007-02-16 11:25 139K anoCar1.agp.gz 2007-03-21 14:13 1.2M anoCar1.WMSdust.bed.gz 2007-02-16 16:57 54M anoCar1.2bit 2007-02-17 09:15 489M