This directory contains the Drosophila pseudoobscura Flybase
Release 1.0 assembly (Nov. 2004).
The annotations are from UCSC and collaborators worldwide.
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/dp3/bigZips. To download multiple files, use
the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
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dp3.2bit - contains the complete D. pseudoobscura/dp3 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
chromFa.zip - The assembly sequence chromosome in one file per
chromosome. 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. RepeatMasker March 2004 version with
RepBase libraries: RepBase Update 8.4, RM database version
20040225.
chromFaMasked.zip - The assembly sequence in one file per
chromosome. Repeats are masked by capital Ns and non-repeating
sequence is shown in upper case.
chromOut.zip - RepeatMasker .out file for chromosomes. These were done
with RepeatMasker at the -s sensitive setting.
chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, translated into one .bed file
per chromosomes.
est.fa.gz - D. pseudoobscura ESTs in GenBank. This sequence data is updated
once a week via automatic GenBank updates.
md5sum.txt - MD5 checksum of these files to verify correct transmission.
mrna.fa .gz - D. pseudoobscura 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.
Name Last modified Size Description
Parent Directory -
dp3.2bit 2004-11-15 23:36 35M
dp3.chrom.sizes 2004-11-16 10:36 336
chromOut.zip 2004-11-16 14:04 2.8M
chromFa.zip 2004-11-16 14:06 41M
chromTrf.zip 2004-11-16 14:06 926K
chromFaMasked.zip 2004-11-16 14:16 39M
md5sum.txt 2014-02-03 11:49 235
xenoMrna.fa.gz 2016-03-18 16:52 5.0G
xenoMrna.fa.gz.md5 2016-03-18 16:53 49
mrna.fa.gz 2019-10-15 16:58 100K
mrna.fa.gz.md5 2019-10-15 16:58 45
est.fa.gz 2019-10-15 17:02 13M
est.fa.gz.md5 2019-10-15 17:02 44
xenoRefMrna.fa.gz 2019-10-15 17:02 331M
xenoRefMrna.fa.gz.md5 2019-10-15 17:02 52
dp3.fa.gz 2020-01-23 02:21 41M