This directory contains compressed phastCons scores for multiple
alignments of the following assemblies to the Mouse May 2004 (mm5)
genome:
- Rat Jun. 2003 (rn3)
- Human May 2004 (hg17)
- Dog Jul. 2004 (canFam1)
- Chicken Feb. 2004 (galGal2)
Each mouse chromosome has a corresponding data file. When uncompressed,
the data file contains two columns: a one-based coordinate and a score
showing the posterior probability that phastCons's phylogenetic hidden
Markov model (HMM) is in its most-conserved state at that base position.
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If you plan to download a large file or multiple files from this
directory, we recommend 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/mm5/phastCons/mzRn3Hg17Cf1Gg2/. To download
multiple files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
All the tables in this directory are freely usable for any
purpose. For data use restrictions regarding the dog and chicken genomes,
see http://genome.ucsc.edu/goldenPath/credits.html.
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References for phastCons:
Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M.,
Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S.,
Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W.,
and Haussler, D. Evolutionarily conserved elements in vertebrate, insect,
worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
(http://www.genome.org/cgi/doi/10.1101/gr.3715005)
Siepel, A. and Haussler, D. Phylogenetic hidden Markov models.
In R. Nielsen, ed., Statistical Methods in Molecular Evolution,
Springer (in press) (2004).
For a discussion of the methods used to calculate the phastCons scores,
see the description page for the Conservation track in the Genome
Browser.
Name Last modified Size Description
Parent Directory -
chr1.gz 2004-10-11 11:26 631M
chr2.gz 2004-10-11 11:36 630M
chr3.gz 2004-10-11 11:43 507M
chr4.gz 2004-10-11 11:51 505M
chr6.gz 2004-10-11 12:07 488M
chr5.gz 2004-10-11 11:59 487M
chrX.gz 2004-10-11 12:33 428M
chr11.gz 2004-10-11 12:49 428M
chr7.gz 2004-10-11 12:13 427M
chr8.gz 2004-10-11 12:20 423M
chr10.gz 2004-10-11 12:43 422M
chr9.gz 2004-10-11 12:26 419M
chr12.gz 2004-10-11 12:55 379M
chr14.gz 2004-10-11 13:07 379M
chr13.gz 2004-10-11 13:01 375M
chr15.gz 2004-10-11 13:12 340M
chr16.gz 2004-10-11 13:18 320M
chr18.gz 2004-10-11 13:27 297M
chr17.gz 2004-10-11 13:22 291M
chr19.gz 2004-10-11 13:30 203M
chrUn_random.gz 2004-10-11 13:33 126M
chrY.gz 2004-10-11 12:34 75M
chr4_random.gz 2004-10-11 12:35 22M
chr2_random.gz 2004-10-11 12:35 21M
chrX_random.gz 2004-10-11 12:36 18M
chr7_random.gz 2004-10-11 12:36 17M
chr5_random.gz 2004-10-11 12:35 6.0M
chr3_random.gz 2004-10-11 12:35 5.6M
chr12_random.gz 2004-10-11 13:30 4.8M
chr14_random.gz 2004-10-11 13:30 4.6M
chr13_random.gz 2004-10-11 13:30 4.1M
chr6_random.gz 2004-10-11 12:35 3.6M
chr8_random.gz 2004-10-11 12:36 3.3M
chr1_random.gz 2004-10-11 12:34 3.2M
chr18_random.gz 2004-10-11 13:30 3.0M
chr16_random.gz 2004-10-11 13:30 2.9M
chr17_random.gz 2004-10-11 13:30 2.5M
chr9_random.gz 2004-10-11 12:36 1.5M
chr15_random.gz 2004-10-11 13:30 1.4M
chr19_random.gz 2004-10-11 13:30 1.4M
chr10_random.gz 2004-10-11 13:30 1.0M
chrY_random.gz 2004-10-11 12:36 738K
chrM.gz 2004-10-11 12:26 54K
md5sum.txt 2004-10-11 14:03 1.9K