This directory contains the May 2010 (Broad AnoCar2.0/anoCar2) assembly of the lizard genome (anoCar2, Broad Institute of MIT and Harvard AnoCar 2.0 (GCA_000090745.1)), 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/models/anole/ WGS assembly information: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAWZ02 Files included in this directory: anoCar2.2bit - contains the complete lizard/anoCar2 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 anoCar2.agp.gz - Description of how the assembly was generated from fragments. anoCar2.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. anoCar2.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. anoCar2.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. RepeatMasker version: June 30 2010 (open-3-2-9) anoCar2.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. est.fa.gz - Lizard ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. 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. anoCar2.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. anoCar2.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used - to construct the GC Percent track anoCar2.gc5Base.wig.gz - wiggle database table for the GC Percent track - this is an older standard alternative to the current - bigWig format of the track, sometimes usefull for analysis anoCar2.gc5Base.wib - binary data to correspond with the gc5Base.wig file see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database for a discussion of how to use the wig.gz and .wib files for interaction with the GC percent data values anoCar2.chromAlias.txt - sequence name alias file, one line for each sequence name. First column is sequence name followed by tab separated alias names. ------------------------------------------------------------------ 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 [username: anonymous, password: your email address], then cd to the directory goldenPath/anoCar2/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) Alternate methods to ftp access. Using an rsync command to download the entire directory: rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/bigZips/chromFa.tar.gz' -O chromFa.tar.gz To unpack the *.tar.gz files: tar xvzf <file>.tar.gz To uncompress the fa.gz files: gunzip <file>.fa.gz The Lizard sequence is made freely 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 provider of these data (The Broad Institute) is properly acknowledged. 3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). 4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - anoCar2.2bit 2011-04-13 10:08 492M anoCar2.agp.gz 2011-04-14 16:04 1.0M anoCar2.chrom.sizes 2011-04-12 15:15 148K anoCar2.chromAlias.txt 2020-09-29 10:46 351K anoCar2.fa.gz 2011-04-14 16:13 544M anoCar2.fa.masked.gz 2011-04-14 16:19 345M anoCar2.fa.out.gz 2011-04-14 16:04 36M anoCar2.gc5Base.wib 2019-01-17 14:44 327M anoCar2.gc5Base.wig.gz 2019-01-17 14:44 6.6M anoCar2.gc5Base.wigVarStep.gz 2011-04-12 15:21 861M anoCar2.trf.bed.gz 2011-04-14 16:05 5.5M est.fa.gz 2020-09-09 17:15 40M est.fa.gz.md5 2020-09-09 17:15 44 genes/ 2020-10-02 13:37 - md5sum.txt 2019-01-17 15:50 479 mrna.fa.gz 2020-09-09 17:00 48K mrna.fa.gz.md5 2020-09-09 17:00 45 upstream1000.fa.gz 2020-09-09 17:15 1.9M upstream1000.fa.gz.md5 2020-09-09 17:15 53 upstream2000.fa.gz 2020-09-09 17:15 3.7M upstream2000.fa.gz.md5 2020-09-09 17:15 53 upstream5000.fa.gz 2020-09-09 17:16 8.7M upstream5000.fa.gz.md5 2020-09-09 17:16 53 xenoMrna.fa.gz 2020-09-09 17:10 7.0G xenoMrna.fa.gz.md5 2020-09-09 17:10 49 xenoRefMrna.fa.gz 2020-09-09 17:15 344M xenoRefMrna.fa.gz.md5 2020-09-09 17:15 52