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:
http://www.broad.mit.edu/mammals/
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
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
felCat3.agp.gz - Description of how the assembly was generated from
fragments.
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
upper case.
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
format.
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.
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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)
Name Last modified Size Description
Parent Directory -
est.fa.gz 2019-10-17 03:34 177K
est.fa.gz.md5 2019-10-17 03:34 44
felCat3.2bit 2006-10-17 10:18 1.0G
felCat3.agp.gz 2006-10-20 12:35 17M
felCat3.chrom.sizes 2006-10-05 10:37 4.3M
felCat3.fa.gz 2006-10-20 12:43 559M
felCat3.fa.masked.gz 2006-10-20 12:50 368M
felCat3.fa.out.gz 2006-10-20 12:36 95M
felCat3.quals.fa.gz 2006-10-05 10:19 458M
felCat3.trf.bed.gz 2006-10-20 12:36 5.2M
genes/ 2020-02-05 13:47 -
md5sum.txt 2014-01-03 16:15 358
mrna.fa.gz 2019-10-17 03:30 1.0M
mrna.fa.gz.md5 2019-10-17 03:30 45
refMrna.fa.gz 2019-10-17 03:35 236K
refMrna.fa.gz.md5 2019-10-17 03:35 48
upstream1000.fa.gz 2019-10-17 03:36 20
upstream1000.fa.gz.md5 2019-10-17 03:36 53
upstream2000.fa.gz 2019-10-17 03:37 20
upstream2000.fa.gz.md5 2019-10-17 03:37 53
upstream5000.fa.gz 2019-10-17 03:38 20
upstream5000.fa.gz.md5 2019-10-17 03:38 53
xenoMrna.fa.gz 2016-03-15 04:24 5.0G
xenoMrna.fa.gz.md5 2016-03-15 04:24 49
xenoRefMrna.fa.gz 2019-10-17 03:35 331M
xenoRefMrna.fa.gz.md5 2019-10-17 03:35 52