This directory contains the Release 3.1 (Jan. 2003, UCSC version dm1) assembly of the Drosophila melanogaster genome (dm1). 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. 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. 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. dm1.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/dm1/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 2003-10-29 13:47 39M chromFaMasked.zip 2003-10-29 13:51 34M chromOut.zip 2003-10-29 13:45 2.1M chromTrf.zip 2003-10-29 13:51 286K dm1.2bit 2014-04-30 10:28 31M dm1.2bit.md5 2014-05-07 15:24 43 dm1.chrom.sizes 2003-10-05 13:29 154 dm1.fa.gz 2020-01-23 02:21 39M est.fa.gz 2020-02-28 00:13 109M est.fa.gz.md5 2020-02-28 00:13 44 mrna.fa.gz 2020-02-28 00:08 40M mrna.fa.gz.md5 2020-02-28 00:08 45 refMrna.fa.gz 2020-02-28 00:13 29M refMrna.fa.gz.md5 2020-02-28 00:13 48 xenoMrna.fa.gz 2016-03-14 15:09 4.9G xenoMrna.fa.gz.md5 2016-03-14 15:09 49 xenoRefMrna.fa.gz 2020-02-28 00:13 308M xenoRefMrna.fa.gz.md5 2020-02-28 00:13 52