This directory contains the Drosophila persimilis 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.
droPer1.2bit - contains the complete D. persimilis/droPer1 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.
droPer1.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/droPer1/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/droPer1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/droPer1/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/droPer1/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/droPer1/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 -
xenoMrna.fa.gz.md5 2016-03-19 02:25 49
xenoRefMrna.fa.gz.md5 2019-10-15 17:23 52
md5sum.txt 2014-01-03 16:38 247
droPer1.chrom.sizes 2005-11-23 21:08 201K
droPer1.chromAlias.txt 2022-09-08 14:11 466K
scaffoldTrf.gz 2005-11-23 21:13 1.1M
droPer1.chromAlias.bb 2022-09-08 14:11 2.7M
scaffoldOut.gz 2005-11-23 21:12 4.2M
scaffoldFaMasked.gz 2006-05-31 14:33 46M
droPer1.2bit 2005-11-23 21:07 47M
scaffoldFa.gz 2005-11-23 21:13 54M
droPer1.fa.gz 2020-01-23 02:21 54M
xenoRefMrna.fa.gz 2019-10-15 17:23 331M
xenoMrna.fa.gz 2016-03-19 02:24 5.0G