Schema for GlimmerHMM - GlimmerHMM Gene Predictions

JavaScript is disabled in your web browser

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

Schema for GlimmerHMM - GlimmerHMM Gene Predictions

Database: DpseGB3 Primary Table: glimmer Row Count: 21,009 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	CH379058.path1.gene2	`varchar(255)`	values
`chrom`	CH379058	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	2856	`int(10) unsigned`	range
`txEnd`	10276	`int(10) unsigned`	range
`cdsStart`	2856	`int(10) unsigned`	range
`cdsEnd`	10276	`int(10) unsigned`	range
`exonCount`	9	`int(10) unsigned`	range
`exonStarts`	2856,3913,6145,6228,6924,81...	`longblob`
`exonEnds`	3006,4017,6200,6540,6965,82...	`longblob`
`score`	0	`int(11)`	range
`name2`	CH379058.path1.gene2	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,0,2,0,0,2,0,1,2,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	CH379058.path1.gene2	CH379058	+	2856	10276	2856	10276	9	2856,3913,6145,6228,6924,8127,9558,9697,10191,	3006,4017,6200,6540,6965,8227,9598,9953,10276,	0	CH379058.path1.gene2	unk	unk	0,0,2,0,0,2,0,1,2,
585	CH379058.path1.gene3	CH379058	-	12617	22628	12617	22628	4	12617,13346,13652,17139,	12718,13434,13794,22628,	0	CH379058.path1.gene3	unk	unk	1,0,2,0,
585	CH379058.path1.gene4	CH379058	-	25361	31416	25361	31416	2	25361,31281,	25850,31416,	0	CH379058.path1.gene4	unk	unk	0,0,
585	CH379058.path1.gene5	CH379058	-	33773	34223	33773	34223	1	33773,	34223,	0	CH379058.path1.gene5	unk	unk	0,
585	CH379058.path1.gene6	CH379058	+	37294	49327	37294	49327	7	37294,38951,41697,44889,45839,47902,49081,	37335,39084,41990,45343,46091,48220,49327,	0	CH379058.path1.gene6	unk	unk	0,2,0,2,0,0,0,
585	CH379058.path1.gene7	CH379058	-	53109	53478	53109	53478	1	53109,	53478,	0	CH379058.path1.gene7	unk	unk	0,
585	CH379058.path1.gene8	CH379058	+	55758	59364	55758	59364	7	55758,56117,56287,56504,57379,57841,58972,	55958,56243,56440,56584,57776,58509,59364,	0	CH379058.path1.gene8	unk	unk	0,2,2,2,1,2,1,
585	CH379058.path1.gene9	CH379058	-	61562	63161	61562	63161	1	61562,	63161,	0	CH379058.path1.gene9	unk	unk	0,
585	CH379058.path1.gene10	CH379058	+	65197	69479	65197	69479	2	65197,68601,	65324,69479,	0	CH379058.path1.gene10	unk	unk	0,1,
585	CH379058.path1.gene11	CH379058	-	72104	76973	72104	76973	7	72104,74335,74559,75375,75584,75859,76930,	72160,74417,74715,75522,75770,76029,76973,	0	CH379058.path1.gene11	unk	unk	1,0,0,0,0,1,0,

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.