This directory contains the Drosophila virilis 12 July 2004 assembly
from Agencourt Bioscience Corporation.
Files included in this directory:
md5sum.txt - MD5 checksum of these files to verify correct transmission.
droVir1.2bit - contains the complete D. virilis/droVir1 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
mrna.fa.gz - D. virilis 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
per scaffold.
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.
droVir1.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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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/droVir1/bigZips. To download multiple files, use the "mget"
command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
These data have been freely provided by Agencourt Bioscience Corporation
before publication for use in the UCSC Genome Browser with the following
understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing particular
genes and regions, provided that the Agencourt is properly acknowledged.
3. Agencourt reserves the right to publish the initial large-scale analyses
of the dataset, including large-scale identification of regions of
evolutionary conservation and large-scale genomic assembly.
4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory -
droVir1.2bit 2004-11-07 15:47 50M
droVir1.chrom.sizes 2004-11-05 11:49 525K
droVir1.fa.gz 2020-01-23 02:21 57M
md5sum.txt 2014-02-03 11:48 251
mrna.fa.gz 2019-10-17 02:12 54K
mrna.fa.gz.md5 2019-10-17 02:12 45
scaffoldFa.zip 2005-03-21 15:17 57M
scaffoldFaMasked.zip 2005-03-21 15:18 49M
scaffoldOut.zip 2004-11-07 17:32 6.1M
scaffoldTrf.zip 2004-11-07 17:35 1.1M
xenoMrna.fa.gz 2016-03-14 19:40 5.0G
xenoMrna.fa.gz.md5 2016-03-14 19:40 49
xenoRefMrna.fa.gz 2019-10-17 02:12 331M
xenoRefMrna.fa.gz.md5 2019-10-17 02:12 52