Schema for GlimmerHMM - GlimmerHMM Gene Predictions

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Schema for GlimmerHMM - GlimmerHMM Gene Predictions

Database: DserGB1 Primary Table: glimmer Row Count: 20,091 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	MTTC01000001.path1.gene1	`varchar(255)`	values
`chrom`	MTTC01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	357	`int(10) unsigned`	range
`txEnd`	2533	`int(10) unsigned`	range
`cdsStart`	357	`int(10) unsigned`	range
`cdsEnd`	2533	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	357,2509,	`longblob`
`exonEnds`	2484,2533,	`longblob`
`score`	0	`int(11)`	range
`name2`	MTTC01000001.path1.gene1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	MTTC01000001.path1.gene1	MTTC01000001	+	357	2533	357	2533	2	357,2509,	2484,2533,	0	MTTC01000001.path1.gene1	unk	unk	0,0,
585	MTTC01000001.path1.gene2	MTTC01000001	-	4697	4985	4697	4985	1	4697,	4985,	0	MTTC01000001.path1.gene2	unk	unk	0,
585	MTTC01000001.path1.gene3	MTTC01000001	+	7130	7364	7130	7364	1	7130,	7364,	0	MTTC01000001.path1.gene3	unk	unk	0,
585	MTTC01000001.path1.gene4	MTTC01000001	+	10058	11105	10058	11105	3	10058,10497,10973,	10217,10587,11105,	0	MTTC01000001.path1.gene4	unk	unk	0,0,0,
585	MTTC01000001.path1.gene5	MTTC01000001	+	13287	14326	13287	14326	2	13287,14125,	13854,14326,	0	MTTC01000001.path1.gene5	unk	unk	0,0,
585	MTTC01000001.path1.gene6	MTTC01000001	+	16724	19179	16724	19179	3	16724,18118,19139,	17231,19098,19179,	0	MTTC01000001.path1.gene6	unk	unk	0,0,2,
585	MTTC01000001.path1.gene7	MTTC01000001	-	21379	21664	21379	21664	1	21379,	21664,	0	MTTC01000001.path1.gene7	unk	unk	0,
585	MTTC01000002.path1.gene1	MTTC01000002	-	220	436	220	436	1	220,	436,	0	MTTC01000002.path1.gene1	unk	unk	0,
585	MTTC01000002.path1.gene2	MTTC01000002	-	2648	2816	2648	2816	1	2648,	2816,	0	MTTC01000002.path1.gene2	unk	unk	0,
585	MTTC01000002.path1.gene3	MTTC01000002	-	4858	5272	4858	5272	1	4858,	5272,	0	MTTC01000002.path1.gene3	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.