Schema for GlimmerHMM - GlimmerHMM Gene Predictions

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Schema for GlimmerHMM - GlimmerHMM Gene Predictions

Database: DkikGB2 Primary Table: glimmer Row Count: 27,192

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	AFFH02000049.path1.gene1	`varchar(255)`	values
`chrom`	AFFH02000049	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	479	`int(10) unsigned`	range
`txEnd`	519	`int(10) unsigned`	range
`cdsStart`	479	`int(10) unsigned`	range
`cdsEnd`	519	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	479,	`longblob`
`exonEnds`	519,	`longblob`
`score`	0	`int(11)`	range
`name2`	AFFH02000049.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	AFFH02000049.path1.gene1	AFFH02000049	-	479	519	479	519	1	479,	519,	0	AFFH02000049.path1.gene1	incmpl	incmpl	0,
585	AFFH02000063.path1.gene1	AFFH02000063	+	28	169	28	169	1	28,	169,	0	AFFH02000063.path1.gene1	incmpl	incmpl	0,
585	AFFH02000063.path1.gene2	AFFH02000063	-	1189	1480	1189	1480	1	1189,	1480,	0	AFFH02000063.path1.gene2	incmpl	incmpl	0,
585	AFFH02000074.path1.gene1	AFFH02000074	+	1473	1561	1473	1561	1	1473,	1561,	0	AFFH02000074.path1.gene1	incmpl	incmpl	0,
585	AFFH02000086.path1.gene1	AFFH02000086	-	205	367	205	367	1	205,	367,	0	AFFH02000086.path1.gene1	incmpl	incmpl	0,
585	AFFH02000086.path1.gene2	AFFH02000086	+	1678	1941	1678	1941	1	1678,	1941,	0	AFFH02000086.path1.gene2	incmpl	incmpl	0,
585	AFFH02000093.path1.gene1	AFFH02000093	-	421	637	421	637	1	421,	637,	0	AFFH02000093.path1.gene1	incmpl	incmpl	0,
585	AFFH02000110.path1.gene1	AFFH02000110	+	5037	5063	5037	5063	1	5037,	5063,	0	AFFH02000110.path1.gene1	incmpl	incmpl	0,
585	AFFH02000114.path1.gene1	AFFH02000114	-	951	1167	951	1167	1	951,	1167,	0	AFFH02000114.path1.gene1	incmpl	incmpl	0,
585	AFFH02000140.path1.gene1	AFFH02000140	-	10058	10112	10058	10112	1	10058,	10112,	0	AFFH02000140.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.