This directory contains the Apis mellifera Amel_1.2 assembly (apiMel1, Jul. 2004) from the Baylor College of Medicine HGSC Honey Bee Genome Project. For more information, see the Baylor website: http://www.hgsc.bcm.tmc.edu/projects/honeybee/. Files included in this directory: md5sum.txt - Checksums of the files in this directory. apiMel1.2bit - contains the complete A. mellifera/apiMel1 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 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 Ns 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. apiMel1.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/apiMel1/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) For conditions of use regarding these data, see http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html.
Name Last modified Size Description
Parent Directory - apiMel1.2bit 2004-11-08 15:17 54M apiMel1.chrom.sizes 2004-11-08 15:20 171K apiMel1.fa.gz 2020-01-23 02:17 62M est.fa.gz 2019-10-16 18:09 13M est.fa.gz.md5 2019-10-16 18:09 44 md5sum.txt 2014-02-03 11:03 251 mrna.fa.gz 2019-10-16 18:03 51M mrna.fa.gz.md5 2019-10-16 18:03 45 scaffoldFa.zip 2004-11-08 15:55 62M scaffoldFaMasked.zip 2004-11-08 15:57 56M scaffoldOut.zip 2004-11-08 15:53 17M scaffoldTrf.zip 2004-11-08 15:57 1.0M xenoMrna.fa.gz 2016-03-22 08:35 4.9G xenoMrna.fa.gz.md5 2016-03-22 08:35 49 xenoRefMrna.fa.gz 2019-10-16 18:09 330M xenoRefMrna.fa.gz.md5 2019-10-16 18:09 52