This directory contains the Feb. 2007 assembly of the lizard genome (anoCar1, Broad Institute AnoCar (1.0)), as well as repeat annotations and GenBank sequences. This assembly was produced by the Broad Institute at MIT and Harvard. For more information on the lizard genome, see the project website: http://www.broad.mit.edu/tools/data/data-vert.html Files included in this directory: anoCar1.2bit - contains the complete lizard/anoCar1 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 anoCar1.agp.gz - Description of how the assembly was generated from fragments. anoCar1.fa.gz - "Soft-masked" assembly sequence in one file. Repeats from WindowMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. Note, this sequence is *not* masked with the RepeatMasker .out specification. anoCar1.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. anoCar1.WMSdust.bed.gz - Repeat areas identified by WindowMasker with the -sdust option. anoCar1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. RepeatMasker version: October 6, 2006 (open-3-1-6) with RepBase libraries: RepBase Update 20061006. anoCar1.qual.qv.gz - base by base qual scores for anoCar1 assembly. Values vary from 0 to 60. anoCar1.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. anoCar1.quals.fa.gz - quality scores in fasta file format md5sum.txt - checksums of files in this directory mrna.fa.gz - Lizard 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. anoCar1.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/anoCar1/bigZips. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory)