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 -
md5sum.txt 11-Oct-2004 14:03 1.9K
chrY_random.gz 11-Oct-2004 12:36 738K
chrY.gz 11-Oct-2004 12:34 75M
chrX_random.gz 11-Oct-2004 12:36 18M
chrX.gz 11-Oct-2004 12:33 428M
chrUn_random.gz 11-Oct-2004 13:33 126M
chrM.gz 11-Oct-2004 12:26 54K
chr19_random.gz 11-Oct-2004 13:30 1.4M
chr19.gz 11-Oct-2004 13:30 203M
chr18_random.gz 11-Oct-2004 13:30 3.0M
chr18.gz 11-Oct-2004 13:27 297M
chr17_random.gz 11-Oct-2004 13:30 2.5M
chr17.gz 11-Oct-2004 13:22 291M
chr16_random.gz 11-Oct-2004 13:30 2.9M
chr16.gz 11-Oct-2004 13:18 320M
chr15_random.gz 11-Oct-2004 13:30 1.4M
chr15.gz 11-Oct-2004 13:12 340M
chr14_random.gz 11-Oct-2004 13:30 4.6M
chr14.gz 11-Oct-2004 13:07 379M
chr13_random.gz 11-Oct-2004 13:30 4.1M
chr13.gz 11-Oct-2004 13:01 375M
chr12_random.gz 11-Oct-2004 13:30 4.8M
chr12.gz 11-Oct-2004 12:55 379M
chr11.gz 11-Oct-2004 12:49 428M
chr10_random.gz 11-Oct-2004 13:30 1.0M
chr10.gz 11-Oct-2004 12:43 422M
chr9_random.gz 11-Oct-2004 12:36 1.5M
chr9.gz 11-Oct-2004 12:26 419M
chr8_random.gz 11-Oct-2004 12:36 3.3M
chr8.gz 11-Oct-2004 12:20 423M
chr7_random.gz 11-Oct-2004 12:36 17M
chr7.gz 11-Oct-2004 12:13 427M
chr6_random.gz 11-Oct-2004 12:35 3.6M
chr6.gz 11-Oct-2004 12:07 488M
chr5_random.gz 11-Oct-2004 12:35 6.0M
chr5.gz 11-Oct-2004 11:59 487M
chr4_random.gz 11-Oct-2004 12:35 22M
chr4.gz 11-Oct-2004 11:51 505M
chr3_random.gz 11-Oct-2004 12:35 5.6M
chr3.gz 11-Oct-2004 11:43 507M
chr2_random.gz 11-Oct-2004 12:35 21M
chr2.gz 11-Oct-2004 11:36 630M
chr1_random.gz 11-Oct-2004 12:34 3.2M
chr1.gz 11-Oct-2004 11:26 631M