This directory contains the April 2005 Spur_0.5 release of the S. purpuratus genome (strPur1) obtained from the Baylor College of Medicine Human Genome Sequencing Center. Files included in this directory: strPur1.2bit - contains the complete S. purpuratus/strPur1 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 allAgp.tar.gz - Description of how the assembly was generated from fragments. allFa.tar.gz- Sequences downloaded from Baylor 19 April 2005. allFaMasked.tar.gz - The assembly sequence with repeats masked by capital Ns; non-repeating sequence is shown in upper case. allOut.tar.gz - RepeatMasker .out file for chromosomes. These were created by RepeatMasker at the -s sensitive setting. allTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into one .bed file per chromosomes. md5sum.txt - Checksum file. mrna.fa.gz - S. purpuratus 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. strPur1.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/strPur1/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) These data are made available before scientific publication with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of these data are properly acknowledged. Please cite the BCM-HGSC web site or publications from BCM-HGSC referring to the genome sequence. 3. BCM HGSC plans to publish the assembly and genomic annotation of the dataset, including large-scale identification of regions of evolutionary conservation. 4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement. 5. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - allAgp.tar.gz 2006-02-22 12:07 5.2M allFa.tar.gz 2006-02-22 12:41 494M allFaMasked.tar.gz 2006-02-22 12:56 246M allOut.tar.gz 2006-02-22 16:43 19M allTrf.tar.gz 2006-02-22 12:56 4.0M md5sum.txt 2013-12-10 14:49 336 mrna.fa.gz 2019-10-17 21:17 28M mrna.fa.gz.md5 2019-10-17 21:17 45 refMrna.fa.gz 2019-10-17 21:18 380K refMrna.fa.gz.md5 2019-10-17 21:18 48 strPur1.2bit 2005-07-16 02:18 274M strPur1.chrom.sizes 2005-04-19 02:47 8.2M strPur1.fa.gz 2020-01-23 02:26 254M xenoMrna.fa.gz 2016-02-27 12:11 4.9G xenoMrna.fa.gz.md5 2016-02-27 12:12 49 xenoRefMrna.fa.gz 2019-10-17 21:18 330M xenoRefMrna.fa.gz.md5 2019-10-17 21:18 52