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: DanaCAF1 Primary Table: glimmer Row Count: 17,436 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_0.path1.gene1	`varchar(255)`	values
`chrom`	scaffold_0	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	157	`int(10) unsigned`	range
`txEnd`	346	`int(10) unsigned`	range
`cdsStart`	157	`int(10) unsigned`	range
`cdsEnd`	346	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	157,	`longblob`
`exonEnds`	346,	`longblob`
`score`	0	`int(11)`	range
`name2`	scaffold_0.path1.gene1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`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	scaffold_0.path1.gene1	scaffold_0	+	157	346	157	346	1	157,	346,	0	scaffold_0.path1.gene1	unk	unk	0,
585	scaffold_10080.path1.gene1	scaffold_10080	+	3185	3320	3185	3320	1	3185,	3320,	0	scaffold_10080.path1.gene1	unk	unk	0,
585	scaffold_10103.path1.gene1	scaffold_10103	-	3136	3549	3136	3549	2	3136,3250,	3188,3549,	0	scaffold_10103.path1.gene1	unk	unk	2,0,
585	scaffold_10209.path1.gene1	scaffold_10209	-	540	4714	540	4714	3	540,3254,4607,	691,3335,4714,	0	scaffold_10209.path1.gene1	unk	unk	2,2,0,
585	scaffold_10210.path1.gene1	scaffold_10210	+	5320	5605	5320	5605	1	5320,	5605,	0	scaffold_10210.path1.gene1	unk	unk	0,
585	scaffold_10211.path1.gene1	scaffold_10211	-	852	4982	852	4982	2	852,4829,	879,4982,	0	scaffold_10211.path1.gene1	unk	unk	0,0,
585	scaffold_10214.path1.gene1	scaffold_10214	-	1597	2064	1597	2064	1	1597,	2064,	0	scaffold_10214.path1.gene1	unk	unk	0,
585	scaffold_10220.path1.gene1	scaffold_10220	-	848	3823	848	3823	3	848,1118,3801,	988,1214,3823,	0	scaffold_10220.path1.gene1	unk	unk	1,1,0,
585	scaffold_10296.path1.gene1	scaffold_10296	+	265	1246	265	1246	2	265,970,	590,1246,	0	scaffold_10296.path1.gene1	unk	unk	0,1,
585	scaffold_103.path1.gene1	scaffold_103	+	2327	2468	2327	2468	1	2327,	2468,	0	scaffold_103.path1.gene1	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.