This directory contains the Release 4 (Apr. 2004, UCSC version dm2)
assembly of the Drosophila melanogaster genome.
Files included in this directory:
dm1.2bit - contains the complete D. melanogaster/dm1 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
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 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. The main assembly is in the chrN.fa files where N
is the name of the chromosome.
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
created 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 chromosome.
est.fa.gz - D. melanogaster 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. 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 RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it could be slightly out
of sync with the RefSeq data which is updated daily for most
assemblies.
upstream2000.zip - Same as upstream1000, but 2000 bases.
upstream5000.zip - 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.
dm2.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/dm2/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.
Name Last modified Size Description
Parent Directory -
chromFa.zip 2005-01-26 11:49 39M
chromFaMasked.zip 2005-01-26 11:50 34M
chromOut.zip 2005-01-26 11:48 2.2M
chromTrf.zip 2005-01-26 11:50 288K
dm2.2bit 2005-07-03 09:10 32M
dm2.chrom.sizes 2004-09-09 15:37 177
dm2.fa.gz 2020-01-23 02:21 39M
est.fa.gz 2019-10-17 01:30 109M
est.fa.gz.md5 2019-10-17 01:30 44
md5sum.txt 2014-05-05 15:31 280
mrna.fa.gz 2019-10-17 01:14 40M
mrna.fa.gz.md5 2019-10-17 01:14 45
refMrna.fa.gz 2019-10-17 01:30 29M
refMrna.fa.gz.md5 2019-10-17 01:30 48
upstream1000.fa.gz 2019-10-17 01:31 6.0M
upstream1000.fa.gz.md5 2019-10-17 01:31 53
upstream2000.fa.gz 2019-10-17 01:31 11M
upstream2000.fa.gz.md5 2019-10-17 01:31 53
upstream5000.fa.gz 2019-10-17 01:31 24M
upstream5000.fa.gz.md5 2019-10-17 01:31 53
xenoMrna.fa.gz 2019-10-17 01:24 6.7G
xenoMrna.fa.gz.md5 2019-10-17 01:25 49
xenoRefMrna.fa.gz 2019-10-17 01:30 302M
xenoRefMrna.fa.gz.md5 2019-10-17 01:30 52