This directory contains the Drosophila sechellia 28 October 2005 assembly 
from the Broad Institute at MIT and Harvard.  The annotations are from 
UCSC and collaborators worldwide.

Files included in this directory:

md5sum.txt - MD5 checksum of these files to verify correct transmission.

droSec1.2bit - contains the complete D. sechellia/droSec1 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

scaffoldFa.gz - The working draft sequence in one FASTA record per scaffold.
    Repeats from RepeatMasker and Tandem Repeats Finder (with period
    of 12 or less) are in lower case while non-repeating sequence is
    in upper case.  

scaffoldFaMasked.gz - The working draft sequence in one FASTA record per
    scaffold. Repeats are masked by capital N's and non-repeating
    sequence is shown in upper case.

scaffoldOut.gz - RepeatMasker .out file for scaffolds.  These were 
    created with RepeatMasker at the -s sensitive setting.

scaffoldTrf.gz - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, translated into one .bed file. 

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.

droSec1.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 hgdownload.soe.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/droSec1/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.soe.ucsc.edu/goldenPath/droSec1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/droSec1/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/droSec1/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/droSec1/bigZips/chromFa.tar.gz' 
        -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

-----------------------------------------------------------------------------
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 - droSec1.2bit 2005-11-30 12:56 41M droSec1.chrom.sizes 2005-11-30 12:57 233K droSec1.chromAlias.txt 2020-09-29 10:48 320K droSec1.fa.gz 2020-01-23 02:21 47M md5sum.txt 2014-01-03 16:37 247 scaffoldFa.gz 2005-11-30 15:36 47M scaffoldFaMasked.gz 2005-11-30 15:36 38M scaffoldOut.gz 2005-11-30 15:35 3.6M scaffoldTrf.gz 2005-11-30 15:36 233K xenoMrna.fa.gz 2019-10-15 17:33 6.8G xenoMrna.fa.gz.md5 2019-10-15 17:33 49 xenoRefMrna.fa.gz 2019-10-15 17:33 331M xenoRefMrna.fa.gz.md5 2019-10-15 17:33 52