This directory contains the Drosophila pseudoobscura Freeze 1 assembly
(dp2, Aug. 2003) from the Baylor College of Medicine HGSC Drosophila
Files included in this directory:
dp2.2bit - contains the complete D. pseudoobscura/dp2 genome sequence
in the 2bit file format. While we are providing the .2bit for
this assembly, we will continue to use the .nib files in
the Genome Browser. 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
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.
scaffoldFa.zip - The working draft sequence in one file 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. The main assembly is in the chrN.fa files where N
is the name of the scaffold.
scaffoldFaMasked.zip - The working draft sequence in one file per
scaffold. Repeats are masked by capital N's and non-repeating
sequence is shown in upper case.
scaffoldOut.zip - RepeatMasker .out file for scaffolds. These were
created with RepeatMasker at the -s sensitive setting.
scaffoldTrf.zip - 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
dp2.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
If you plan to download a large file or multiple files from this
directory, we recommend 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/dp2/bigZips. To download multiple files, use
the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
All the files in this directory are freely available for public use.
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80