This directory contains the Jul. 2011 (HetGla_1.0/hetGla1) assembly of the naked mole-rat genome (hetGla1, HetGla_1.0 (NCBI project 68323, accession GCA_000230455.1)), as well as repeat annotations and GenBank sequences. This assembly was produced by the National Center for Biotechnology Information (NCBI). For more information on the naked mole-rat genome, see the project website: http://www.ncbi.nlm.nih.gov/bioproject/68323 Files included in this directory: hetGla1.2bit - contains the complete naked mole-rat/hetGla1 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 hetGla1.agp.gz - Description of how the assembly was generated from fragments. hetGla1.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. hetGla1.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. hetGla1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. RepeatMasker version: April 26 2011 (open-3-3-0) (open-3-2-9) RepeatMasker library version: 0110920 hetGla1.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 mrna.fa.gz - Naked mole-rat 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. hetGla1.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. hetGla1.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used - to construct the GC Percent track hetGla1.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 hetGla1.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 hetGla1.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/hetGla1/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/hetGla1/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hetGla1/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hetGla1/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hetGla1/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
Name Last modified Size Description
Parent Directory - genes/ 2020-10-02 13:37 - est.fa.gz 2019-10-17 06:18 20 est.fa.gz.md5 2019-10-17 06:18 44 mrna.fa.gz.md5 2019-10-17 06:04 45 xenoMrna.fa.gz.md5 2019-10-17 06:14 49 xenoRefMrna.fa.gz.md5 2019-10-17 06:18 52 md5sum.txt 2019-01-17 15:54 479 mrna.fa.gz 2019-10-17 06:04 136K hetGla1.chrom.sizes 2011-12-02 15:40 515K hetGla1.chromAlias.txt 2022-09-08 14:12 1.2M hetGla1.trf.bed.gz 2012-01-04 14:07 4.3M hetGla1.agp.gz 2012-01-04 14:06 6.3M hetGla1.chromAlias.bb 2022-09-08 14:12 7.0M hetGla1.gc5Base.wig.gz 2019-01-17 14:49 11M hetGla1.fa.out.gz 2012-01-04 14:07 126M xenoRefMrna.fa.gz 2019-10-17 06:18 331M hetGla1.gc5Base.wib 2019-01-17 14:49 480M hetGla1.fa.masked.gz 2012-01-04 14:29 564M hetGla1.2bit 2011-12-07 09:53 742M hetGla1.fa.gz 2012-01-04 14:19 781M hetGla1.gc5Base.wigVarStep.gz 2011-12-02 15:46 1.2G xenoMrna.fa.gz 2019-10-17 06:14 6.8G