This directory contains the May 2005 assembly of the rabbit genome (oryCun1) obtained from the Broad Institute. More information may be found at http://www.broad.mit.edu/mammals/. Files included in this directory: assembly.agp.gz - Description of how the assembly was generated from fragments. oryCun1.quals.fa.gz - quality scores in fasta file format md5sum.txt - MD5 checksum of these files to verify correct transmission. rmsk.out.gz - RepeatMasker .out file for scaffolds. These were created by RepeatMasker at the -s sensitive setting. scaffold.fa.gz - unmasked scaffolds sequences obtained from the Broad Institute. scaffoldSoftMask.fa.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. RepeatMasker May 3 2005 (open-3-1-0) version with RepBase libraries: RepBase Update 9.11, RM database version 20050112. trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into one .bed file for all the scaffolds. ----------------------------------------------------------------- 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/oryCun1/bigZips. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory)