This directory contains compressed phastCons scores for multiple alignments of the following assemblies to the zebrafish genome (danRer3, May 2005): - Human (hg18, Feb. 2006) - Mouse (mm7, Aug. 2005) - Fugu (fr1, Aug. 2002) - Tetraodon (tetNig1, Feb. 2004) For a description of the phastCons file format, see http://genome.ucsc.edu/goldenPath/help/phastCons.html. ----------------------------------------------------------------- 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/danRer3/phastCons5wayScores. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) All the files in this directory are freely available for public use. For data use restrictions regarding the genome assemblies used in this annotation, see http://genome.ucsc.edu/goldenPath/credits.html. ------------------------------------------------------------- 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 danRer3 Conservation track in the Genome Browser.