This directory contains the Sep. 2006 assembly of the S. purpuratus genome (strPur2, Baylor release 3 Spur 2.1), as well as repeat annotations and GenBank sequences. This assembly was produced by the Baylor College of Medicine Human Genome Sequencing Center. For more information on the S. purpuratus genome, see the project website: http://www.hgsc.bcm.tmc.edu/projects/seaurchin/ Files included in this directory: strPur2.2bit - contains the complete S. purpuratus/strPur2 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 strPur2.agp.gz - Description of how the assembly was generated from fragments. strPur2.fa.gz - "Soft-masked" assembly sequence in one file. 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. strPur2.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. strPur2.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. RepeatMasker version open-3-1-6 Database RepeatMaskerLib.embl version: 20061006. strPur2.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into UCSC's BED format. md5sum.txt - checksums of files in this directory strPur2.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 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/strPur2/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 the S. purpuratus genome sequence data, see http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html .
Name Last modified Size Description
Parent Directory - est.fa.gz 2020-02-27 14:43 34M est.fa.gz.md5 2020-02-27 14:43 44 genes/ 2020-02-05 13:47 - md5sum.txt 2014-01-03 15:20 304 mrna.fa.gz 2020-02-27 14:29 28M mrna.fa.gz.md5 2020-02-27 14:29 45 refMrna.fa.gz 2020-02-27 14:43 381K refMrna.fa.gz.md5 2020-02-27 14:43 48 strPur2.2bit 2007-03-22 14:53 227M strPur2.agp.gz 2007-05-17 13:32 3.6M strPur2.chrom.sizes 2007-03-12 14:59 2.0M strPur2.fa.gz 2007-05-17 13:37 249M strPur2.fa.masked.gz 2007-05-17 13:41 213M strPur2.fa.out.gz 2007-05-17 13:33 24M strPur2.trf.bed.gz 2007-05-17 13:33 3.9M xenoMrna.fa.gz 2020-02-27 14:38 6.8G xenoMrna.fa.gz.md5 2020-02-27 14:38 49 xenoRefMrna.fa.gz 2020-02-27 14:43 336M xenoRefMrna.fa.gz.md5 2020-02-27 14:43 52