This directory contains the March 2006 assembly of the cat genome
(felCat3, Broad Release 3), 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 cat genome, see the project website:
Files included in this directory:
felCat3.2bit - contains the complete cat/felCat3 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
felCat3.agp.gz - Description of how the assembly was generated from
felCat3.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.
felCat3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
felCat3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. RepeatMasker version: March 20, 2006 (open-3-1-5)
with RepBase libraries: RepBase Update 20060315.
felCat3.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
felCat3.quals.fa.gz - quality scores in fasta file format
md5sum.txt - checksums of files in this directory
felCat3.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/felCat3/bigZips. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80