This directory contains the Drosophila pseudoobscura Flybase Release 1.0 assembly (Nov. 2004). The annotations are from UCSC and collaborators worldwide. If you plan 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 to hgdownload.cse.ucsc.edu, then go to the directory goldenPath/dp3/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) ------------------------------------------------------------ dp3.2bit - contains the complete D. pseudoobscura/dp3 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 chromFa.zip - The assembly sequence chromosome 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. RepeatMasker March 2004 version with RepBase libraries: RepBase Update 8.4, RM database version 20040225. 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 done 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 chromosomes. est.fa.gz - D. pseudoobscura 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. pseudoobscura mRNA from GenBank. 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.
Name Last modified Size Description
Parent Directory - chromFa.zip 2004-11-16 14:06 41M chromFaMasked.zip 2004-11-16 14:16 39M chromOut.zip 2004-11-16 14:04 2.8M chromTrf.zip 2004-11-16 14:06 926K dp3.2bit 2004-11-15 23:36 35M dp3.chrom.sizes 2004-11-16 10:36 336 dp3.fa.gz 2020-01-23 02:21 41M est.fa.gz 2020-02-27 05:47 13M est.fa.gz.md5 2020-02-27 05:47 44 md5sum.txt 2014-02-03 11:49 235 mrna.fa.gz 2020-02-27 05:43 100K mrna.fa.gz.md5 2020-02-27 05:43 45 xenoMrna.fa.gz 2016-03-18 16:52 5.0G xenoMrna.fa.gz.md5 2016-03-18 16:53 49 xenoRefMrna.fa.gz 2020-02-27 05:48 337M xenoRefMrna.fa.gz.md5 2020-02-27 05:48 52