This directory contains the Dec. 2008 (NHGRI/GTB V17e/felCat4) assembly of the cat genome (catChrV17e, NHGRI/Genome Technology Branch (NCBI project 10703, accession ACBE0100000)), as well as repeat annotations and GenBank sequences. This assembly was produced by the Agencourt Bioscience Corporation and Hill's Pet Nutrition, Inc.. The mitochondrial genome was sequenced by Laboratory of Genomic Diversity. For more information on the cat genome, see the project website: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=10703 http://www.beckmangenomics.com/ http://www.hillspet.com/ http://home.ncifcrf.gov/ccr/lgd/comparative_genome/catgenome/index_n.asp Files included in this directory: felCat4.2bit - contains the complete cat/felCat4 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 felCat4.agp.gz - Description of how the assembly was generated from fragments. felCat4.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. felCat4.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. felCat4.fa.out.gz - RepeatMasker .out file. (one file per chromosome). RepeatMasker was run with the -s (sensitive) setting. June 4 2009 (open-3-2-8) version of RepeatMasker RepeatMaskerLib.embl version: 20090604; felCat4.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 - Cat 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 - Cat 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. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts of RefSeq genes with annotated 5' UTRs. This file is updated weekly so it might be slightly out of sync with the RefSeq data which is updated daily for most assemblies. upstream2000.fa.gz - Same as upstream1000, but 2000 bases. upstream5000.fa.gz - Same as upstream1000, but 5000 bases. 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. felCat4.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 [username: anonymous, password: your email address], then cd to the directory goldenPath/felCat4/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/felCat4/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/felCat4/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/felCat4/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/felCat4/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 All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory - est.fa.gz 2020-02-28 01:39 177K est.fa.gz.md5 2020-02-28 01:39 44 felCat4.2bit 2010-05-27 01:19 786M felCat4.agp.gz 2010-07-02 09:24 14M felCat4.chrom.sizes 2010-05-26 11:16 2.4M felCat4.fa.gz 2010-07-02 09:36 646M felCat4.fa.masked.gz 2010-07-02 09:44 402M felCat4.fa.out.gz 2010-07-02 09:25 121M felCat4.trf.bed.gz 2010-07-02 09:25 7.7M genes/ 2020-02-05 13:47 - md5sum.txt 2010-07-02 09:45 463 mrna.fa.gz 2020-02-28 01:35 1.0M mrna.fa.gz.md5 2020-02-28 01:35 45 refMrna.fa.gz 2020-02-28 01:40 244K refMrna.fa.gz.md5 2020-02-28 01:40 48 upstream1000.fa.gz 2020-02-28 01:41 56K upstream1000.fa.gz.md5 2020-02-28 01:41 53 upstream2000.fa.gz 2020-02-28 01:41 101K upstream2000.fa.gz.md5 2020-02-28 01:41 53 upstream5000.fa.gz 2020-02-28 01:42 223K upstream5000.fa.gz.md5 2020-02-28 01:42 53 xenoMrna.fa.gz 2016-03-15 02:44 5.0G xenoMrna.fa.gz.md5 2016-03-15 02:44 49 xenoRefMrna.fa.gz 2020-02-28 01:40 336M xenoRefMrna.fa.gz.md5 2020-02-28 01:40 52