This directory contains the Apr. 2006 assembly of the D. melanogaster genome
(dm3, BDGP Release 5), as well as repeat annotations and GenBank sequences.
This assembly was produced by the Berkeley Drosophila Genome Project.
For more information on the D. melanogaster genome, see the release notes:
http://www.fruitfly.org/sequence/release5genomic.shtml
Files included in this directory:
dm3.2bit - contains the complete D. melanogaster/dm3 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
chromAgp.tar.gz - Description of how the assembly was generated from
fragments, unpacking to one file per chromosome.
chromFa.tar.gz - The assembly sequence in one file per chromosome.
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.
chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
RepeatMasker was run with the -s (sensitive) setting.
The May 17 2007 (open-3-1-8) version of RepeatMasker and library release
20061006 were used.
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format (one file per chromosome).
est.fa.gz - D. melanogaster ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - D. melanogaster mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts for FlyBase genes with annotated 5' UTRs.
upstream2000.fa.gz - Same as upstream1000, but 2000 bases.
upstream5000.fa.gz - Same as upstream1000, but 5000 bases.
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.
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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 hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/dm3/bigZips
To download multiple files from the UNIX command line, use the "mget" command.
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Use the "prompt" command to toggle the interactive mode if you do not want
to be prompted for each file that you download.
All the files in this directory are freely available for public use.
Name Last modified Size Description
Parent Directory -
dm3.chrom.sizes 2006-07-10 16:50 228
dm3.2bit 2007-06-21 11:03 42M
chromAgp.tar.gz 2007-06-21 11:05 760K
chromOut.tar.gz 2007-06-21 11:05 4.2M
chromFa.tar.gz 2007-06-21 11:06 49M
chromFaMasked.tar.gz 2007-06-21 11:07 36M
chromTrf.tar.gz 2007-06-21 11:07 413K
md5sum.txt 2014-01-03 15:29 456
mrna.fa.gz 2019-10-17 00:37 40M
mrna.fa.gz.md5 2019-10-17 00:37 45
xenoMrna.fa.gz 2019-10-17 00:48 6.7G
xenoMrna.fa.gz.md5 2019-10-17 00:48 49
est.fa.gz 2019-10-17 00:54 109M
est.fa.gz.md5 2019-10-17 00:54 44
xenoRefMrna.fa.gz 2019-10-17 00:54 302M
xenoRefMrna.fa.gz.md5 2019-10-17 00:54 52
refMrna.fa.gz 2019-10-17 00:54 29M
refMrna.fa.gz.md5 2019-10-17 00:54 48
upstream1000.fa.gz 2019-10-17 00:55 6.4M
upstream1000.fa.gz.md5 2019-10-17 00:55 53
upstream2000.fa.gz 2019-10-17 00:55 13M
upstream2000.fa.gz.md5 2019-10-17 00:55 53
upstream5000.fa.gz 2019-10-17 00:55 35M
upstream5000.fa.gz.md5 2019-10-17 00:55 53
dm3.fa.gz 2020-01-23 02:21 49M
genes/ 2020-02-05 13:47 -