Schema for GlimmerHMM - GlimmerHMM Gene Predictions

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Schema for GlimmerHMM - GlimmerHMM Gene Predictions

Database: DyakCAF1 Primary Table: glimmer Row Count: 19,389 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	chr2L.path1.gene1	`varchar(255)`	values
`chrom`	chr2L	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	349	`int(10) unsigned`	range
`txEnd`	18037	`int(10) unsigned`	range
`cdsStart`	349	`int(10) unsigned`	range
`cdsEnd`	18037	`int(10) unsigned`	range
`exonCount`	10	`int(10) unsigned`	range
`exonStarts`	349,9279,9784,10693,10856,1...	`longblob`
`exonEnds`	549,9722,10427,10799,12048,...	`longblob`
`score`	0	`int(11)`	range
`name2`	chr2L.path1.gene1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,2,1,0,2,0,1,2,1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	chr2L.path1.gene1	chr2L	-	349	18037	349	18037	10	349,9279,9784,10693,10856,12106,14600,16703,17518,17769,	549,9722,10427,10799,12048,12885,14665,17455,17711,18037,	0	chr2L.path1.gene1	unk	unk	1,2,1,0,2,0,1,2,1,0,
585	chr2L.path1.gene2	chr2L	-	20127	29831	20127	29831	13	20127,20966,21194,21490,22503,22905,23238,24171,24943,27591,28097,28211,29220,	20227,21130,21393,21928,22710,23134,23323,24202,25322,27815,28144,28695,29831,	0	chr2L.path1.gene2	unk	unk	2,0,2,2,2,1,0,2,1,2,0,2,0,
585	chr2L.path1.gene3	chr2L	-	32036	38325	32036	38325	5	32036,32502,34333,34969,38316,	32237,33059,34484,35044,38325,	0	chr2L.path1.gene3	unk	unk	0,1,0,0,0,
585	chr2L.path1.gene4	chr2L	-	44299	44482	44299	44482	1	44299,	44482,	0	chr2L.path1.gene4	unk	unk	0,
585	chr2L.path1.gene5	chr2L	+	47714	47909	47714	47909	1	47714,	47909,	0	chr2L.path1.gene5	unk	unk	0,
585	chr2L.path1.gene6	chr2L	+	55280	59389	55280	59389	5	55280,56099,56413,56602,59103,	55348,56277,56545,59046,59389,	0	chr2L.path1.gene6	unk	unk	0,2,0,0,2,
585	chr2L.path1.gene7	chr2L	+	61801	63290	61801	63290	2	61801,62894,	62173,63290,	0	chr2L.path1.gene7	unk	unk	0,0,
585	chr2L.path1.gene8	chr2L	+	65778	67377	65778	67377	2	65778,67150,	66871,67377,	0	chr2L.path1.gene8	unk	unk	0,1,
585	chr2L.path1.gene9	chr2L	-	72463	76726	72463	76726	3	72463,74684,76576,	73485,74727,76726,	0	chr2L.path1.gene9	unk	unk	1,0,0,
585	chr2L.path1.gene10	chr2L	+	81068	81305	81068	81305	1	81068,	81305,	0	chr2L.path1.gene10	unk	unk	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.