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. ------------------------------------------------------------------ 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 - genes/ 2020-02-05 13:47 - est.fa.gz.md5 2020-02-27 23:14 44 mrna.fa.gz.md5 2020-02-27 22:59 45 refMrna.fa.gz.md5 2020-02-27 23:15 48 xenoMrna.fa.gz.md5 2020-02-27 23:09 49 xenoRefMrna.fa.gz.md5 2020-02-27 23:15 52 upstream1000.fa.gz.md5 2020-02-27 23:15 53 upstream2000.fa.gz.md5 2020-02-27 23:15 53 upstream5000.fa.gz.md5 2020-02-27 23:16 53 dm3.chrom.sizes 2006-07-10 16:50 228 md5sum.txt 2014-01-03 15:29 456 chromTrf.tar.gz 2007-06-21 11:07 413K chromAgp.tar.gz 2007-06-21 11:05 760K chromOut.tar.gz 2007-06-21 11:05 4.2M upstream1000.fa.gz 2020-02-27 23:15 6.4M upstream2000.fa.gz 2020-02-27 23:15 13M refMrna.fa.gz 2020-02-27 23:15 29M upstream5000.fa.gz 2020-02-27 23:16 35M chromFaMasked.tar.gz 2007-06-21 11:07 36M mrna.fa.gz 2020-02-27 22:59 40M dm3.2bit 2007-06-21 11:03 42M chromFa.tar.gz 2007-06-21 11:06 49M dm3.fa.gz 2020-01-23 02:21 49M est.fa.gz 2020-02-27 23:14 109M xenoRefMrna.fa.gz 2020-02-27 23:15 308M xenoMrna.fa.gz 2020-02-27 23:09 6.8G