This directory contains the Apr. 2004 freeze of the D. yakuba genome
(droYak1) from the Genome Sequencing Center at Washington University
School of Medicine in St. Louis.
Files included in this directory:
droYak1.2bit - contains the complete D. yakuba/droYak1 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
chromAgp.zip - Description of how the working draft was generated from
fragments at a chromosome layout level.
chromFa.zip - The working draft 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
chromFaMasked.zip - The working draft sequence in one file per
chromosome. Repeats are masked by capital N's 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
est.fa.gz - D. yakuba ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
ms5sum.txt - Checksums of files in this directory.
mrna.fa.gz - D. yakuba 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
droYak1.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/droYak1/bigZips. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
The D. yakuba sequence is made freely available before scientific
publication by The Genome Sequencing Center, WUSTL 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 particular
genes and regions if the providers of these data (Genome Sequencing
Center, WUSTL School of Medicine) are properly acknowledged.
3. The Drosophila yakuba analysis group is aiming to publish an initial
analysis of the D. yakuba genome sequence in 2005 (submitted in early
2005) that will include descriptions of the assembly, genome landscape,
comparative analysis and initial gene content. People who would like to
coordinate other genome-wide analysis with this work should contact
Richard K. Wilson, Genome Sequencing Center Director, Washington
University School of Medicine. We welcome a coordinated approach to
describing this community resource.
4. Any redistribution of the data should carry this notice.
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80