Schema for PhastCons (14 Species) - PhastCons Conserved Elements (14 Drosophila Species)

JavaScript is disabled in your web browser

You must have JavaScript enabled in your web browser to use the Genome Browser

Schema for PhastCons (14 Species) - PhastCons Conserved Elements (14 Drosophila Species)

Database: dm6 Primary Table: dm6_14way_conserved Row Count: 1,758,706

field	example	SQL type
`bin`	585	`smallint(5) unsigned`
`chrom`	chr2L	`varchar(255)`
`chromStart`	5565	`int(10) unsigned`
`chromEnd`	5603	`int(10) unsigned`
`name`	chr2L.1	`varchar(255)`
`score`	0	`int(10) unsigned`
`strand`	+	`char(1)`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand
585	chr2L	5565	5603	chr2L.1	0	+
585	chr2L	5639	5863	chr2L.1	0	+
585	chr2L	7570	7575	chr2L.2	0	+
585	chr2L	7580	7585	chr2L.3	0	+
585	chr2L	7596	7635	chr2L.4	0	+
585	chr2L	7637	7662	chr2L.5	0	+
585	chr2L	7670	7698	chr2L.6	0	+
585	chr2L	7712	7735	chr2L.7	0	+
585	chr2L	7742	7771	chr2L.8	0	+
585	chr2L	7787	7792	chr2L.9	0	+

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

PhastCons (14 Species) (dm6_14way_conserved) Track Description


	Description This track shows predictions of conserved elements produced by the phastCons program. PhastCons is part of the PHAST (PHylogenetic Analysis with Space/Time models) package. The predictions are based on a phylogenetic hidden Markov model (phylo-HMM), a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next. References PhastCons Siepel A, Bejerano G, Pedersen JS, Hinrichs A, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, and Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 15:1034-1050. Chain/Net Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 2003 100(20): 11484-11489. Multiz Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 14(4):708-715. LAST Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93.