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 2020-02-27 23:48 109M est.fa.gz.md5 2020-02-27 23:48 44 md5sum.txt 2014-05-05 15:31 280 mrna.fa.gz 2020-02-27 23:34 40M mrna.fa.gz.md5 2020-02-27 23:34 45 refMrna.fa.gz 2020-02-27 23:49 29M refMrna.fa.gz.md5 2020-02-27 23:49 48 upstream1000.fa.gz 2020-02-27 23:49 6.0M upstream1000.fa.gz.md5 2020-02-27 23:49 53 upstream2000.fa.gz 2020-02-27 23:49 11M upstream2000.fa.gz.md5 2020-02-27 23:49 53 upstream5000.fa.gz 2020-02-27 23:50 24M upstream5000.fa.gz.md5 2020-02-27 23:50 53 xenoMrna.fa.gz 2020-02-27 23:43 6.8G xenoMrna.fa.gz.md5 2020-02-27 23:44 49 xenoRefMrna.fa.gz 2020-02-27 23:49 308M xenoRefMrna.fa.gz.md5 2020-02-27 23:49 52