This directory contains the Sep. 2011 (WUSTL v6.3/melUnd1) assembly of the
budgerigar genome (melUnd1, WUSTL Melopsittacus undulatus Budgerigar Version
6.3 (GCA_000238935.1)), as well as repeat annotations and GenBank sequences.

For more information about this assembly, please note the NCBI resources:

Files included in this directory:

melUnd1.2bit - contains the complete budgerigar/melUnd1 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:
    See also:

melUnd1.agp.gz - Description of how the assembly was generated from

melUnd1.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.

melUnd1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

melUnd1.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.
    April 26 2011 (open-3-3-0) version of RepeatMasker
    RepBase library: RELEASE 20110920

melUnd1.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 - Budgerigar mRNA from GenBank. This sequence data is updated
    once a week via automatic GenBank updates.

melUnd1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

melUnd1.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
melUnd1.gc5Base.wig.gz - wiggle database table for the GC Percent track
                    - this is an older standard alternative to the current
                    - bigWig format of the track, sometimes usefull for analysis
melUnd1.gc5Base.wib    - binary data to correspond with the gc5Base.wig file
    see also:
         for a discussion of how to use the wig.gz and .wib files for
         interaction with the GC percent data values

melUnd1.chromAlias.txt - sequence name alias file, one line
    for each sequence name.  First column is sequence name followed by
    tab separated alias names.

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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/melUnd1/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:// .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync:// .

Or with wget, all files:
    wget --timestamping 
With wget, a single file:
    wget --timestamping 
        -O chromFa.tar.gz

To unpack the *.tar.gz files:
    tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
    gunzip <file>.fa.gz

The Budgerigar sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:

1. The data may be freely downloaded, used in analyses, and repackaged in

2. Users are free to use the data in scientific papers analyzing these data
   if the providers of these data are properly acknowledged.  See for credit information.

3. The centers producing the data reserve the right to publish the initial
   large-scale analyses of the data set, including large-scale identification
   of regions of evolutionary conservation and large-scale genomic assembly.
   Large-scale refers to regions with size on the order of a chromosome (that
   is, 30 Mb or more).

4. Any redistribution of the data should carry this notice.

GenBank Data Usage

The GenBank database is designed to provide and encourage access within 
the scientific community to the most up to date and comprehensive DNA 
sequence information. Therefore, NCBI places no restrictions on the use 
or distribution of the GenBank data. However, some submitters may claim 
patent, copyright, or other intellectual property rights in all or a 
portion of the data they have submitted. NCBI is not in a position to 
assess the validity of such claims, and therefore cannot provide comment 
or unrestricted permission concerning the use, copying, or distribution 
of the information contained in GenBank.
      Name                          Last modified      Size  Description
Parent Directory - genes/ 2020-10-02 13:38 - md5sum.txt 2019-01-17 15:55 479 melUnd1.2bit 2012-03-29 10:17 312M melUnd1.agp.gz 2012-07-13 10:19 1.4M melUnd1.chrom.sizes 2012-03-27 14:10 346K 2022-09-08 14:13 5.9M melUnd1.chromAlias.txt 2022-09-08 14:13 1.1M melUnd1.fa.gz 2012-07-13 10:25 346M melUnd1.fa.masked.gz 2012-07-13 10:31 288M melUnd1.fa.out.gz 2012-07-13 10:19 11M melUnd1.gc5Base.wib 2019-01-17 14:49 209M melUnd1.gc5Base.wig.gz 2019-01-17 14:49 4.7M melUnd1.gc5Base.wigVarStep.gz 2012-03-27 14:14 538M melUnd1.trf.bed.gz 2012-07-13 10:19 707K mrna.fa.gz 2019-10-16 11:11 9.5K mrna.fa.gz.md5 2019-10-16 11:11 45 xenoRefMrna.fa.gz 2019-10-16 11:12 331M xenoRefMrna.fa.gz.md5 2019-10-16 11:12 52