Schema for GlimmerHMM - GlimmerHMM Gene Predictions

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Schema for GlimmerHMM - GlimmerHMM Gene Predictions

Database: DsuzGB1 Primary Table: glimmer Row Count: 31,002

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	AWUT01012676.path1.gene1	`varchar(255)`	values
`chrom`	AWUT01012676	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	6356	`int(10) unsigned`	range
`txEnd`	6408	`int(10) unsigned`	range
`cdsStart`	6356	`int(10) unsigned`	range
`cdsEnd`	6408	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	6356,	`longblob`
`exonEnds`	6408,	`longblob`
`score`	0	`int(11)`	range
`name2`	AWUT01012676.path1.gene1	`varchar(255)`	values
`cdsStartStat`	incmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	incmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	AWUT01012676.path1.gene1	AWUT01012676	-	6356	6408	6356	6408	1	6356,	6408,	0	AWUT01012676.path1.gene1	incmpl	incmpl	0,
585	AWUT01012676.path1.gene2	AWUT01012676	+	11270	44511	11270	44511	7	11270,21536,25217,27818,32565,38554,44438,	11277,21653,25277,27866,32686,38710,44511,	0	AWUT01012676.path1.gene2	incmpl	incmpl	0,1,1,1,1,2,2,
585	AWUT01012676.path1.gene3	AWUT01012676	+	44646	49270	44646	49270	2	44646,49166,	44659,49270,	0	AWUT01012676.path1.gene3	incmpl	incmpl	0,1,
585	AWUT01012676.path1.gene4	AWUT01012676	+	53358	93539	53358	93539	9	53358,58453,63940,65298,70213,79296,86547,92366,93394,	53484,58522,64017,65406,70406,79357,86647,92384,93539,	0	AWUT01012676.path1.gene4	incmpl	incmpl	0,0,0,2,2,0,1,2,2,
585	AWUT01013263.path1.gene1	AWUT01013263	-	7515	7533	7515	7533	1	7515,	7533,	0	AWUT01013263.path1.gene1	incmpl	incmpl	0,
585	AWUT01013263.path1.gene2	AWUT01013263	-	9104	24905	9104	24905	3	9104,16845,24872,	9259,16912,24905,	0	AWUT01013263.path1.gene2	incmpl	incmpl	1,0,0,
585	AWUT01013263.path1.gene3	AWUT01013263	-	24983	54786	24983	54786	5	24983,36536,47256,50391,54757,	25021,36577,47273,50398,54786,	0	AWUT01013263.path1.gene3	incmpl	incmpl	1,2,0,2,0,
585	AWUT01013263.path1.gene4	AWUT01013263	+	55675	55837	55675	55837	1	55675,	55837,	0	AWUT01013263.path1.gene4	incmpl	incmpl	0,
585	AWUT01013263.path1.gene5	AWUT01013263	+	57062	69157	57062	69157	2	57062,69066,	57229,69157,	0	AWUT01013263.path1.gene5	incmpl	incmpl	0,2,
585	AWUT01013449.path1.gene1	AWUT01013449	+	5416	5500	5416	5500	1	5416,	5500,	0	AWUT01013449.path1.gene1	incmpl	incmpl	0,

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

GlimmerHMM (glimmer) Track Description


	Description This track shows predictions from the GlimmerHMM program written by the Center for Bioinformatics and Computational Biology at the University of Maryland. GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). The predictions are based on transcriptional, translational, and donor/acceptor splicing signals, as well as the length and compositional distributions of exons, introns and intergenic regions. References Majoros, W.H., Pertea, M., and Salzberg, S.L. TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders Bioinformatics 20 2878-2879.