Schema for SNAP Genes (BUSCO) - SNAP Gene Predictions with BUSCO Training Set

Database: DsimGB2 Primary Table: snapBUSCO Row Count: 12,462 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	CM002910-snap.1	`varchar(255)`	values
`chrom`	CM002910	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	13983	`int(10) unsigned`	range
`txEnd`	14506	`int(10) unsigned`	range
`cdsStart`	13983	`int(10) unsigned`	range
`cdsEnd`	14506	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	13983,14238,14502,	`longblob`
`exonEnds`	14180,14334,14506,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.CM002910-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	CM002910-snap.1	CM002910	-	13983	14506	13983	14506	3	13983,14238,14502,	14180,14334,14506,	gene.CM002910-snap.1	unk	unk	1,1,0,
585	CM002910-snap.2	CM002910	-	18256	22466	18256	22466	4	18256,19067,19784,22460,	18698,19293,19869,22466,	gene.CM002910-snap.2	unk	unk	2,1,0,0,
585	CM002910-snap.3	CM002910	-	24188	35453	24188	35453	9	24188,25519,26058,26228,27524,28517,30141,30754,35446,	24221,25775,26105,26660,28292,29522,30231,31311,35453,	gene.CM002910-snap.3	unk	unk	0,2,0,0,0,0,0,1,0,
585	CM002910-snap.4	CM002910	+	55799	56364	55799	56364	2	55799,55829,	55807,56364,	gene.CM002910-snap.4	unk	unk	0,2,
585	CM002910-snap.5	CM002910	+	57829	58885	57829	58885	3	57829,58364,58870,	57837,58740,58885,	gene.CM002910-snap.5	unk	unk	0,2,0,
585	CM002910-snap.6	CM002910	+	87433	89866	87433	89866	5	87433,87575,88687,89109,89618,	87440,87681,89010,89538,89866,	gene.CM002910-snap.6	unk	unk	0,1,2,1,1,
585	CM002910-snap.7	CM002910	-	90364	91200	90364	91200	3	90364,90642,91195,	90379,91033,91200,	gene.CM002910-snap.7	unk	unk	0,2,0,
585	CM002910-snap.8	CM002910	-	92047	92774	92047	92774	2	92047,92766,	92708,92774,	gene.CM002910-snap.8	unk	unk	2,0,
585	CM002910-snap.9	CM002910	+	94611	99635	94611	99635	7	94611,94772,96473,96808,97058,98782,99526,	94615,94922,96551,96931,97228,99462,99635,	gene.CM002910-snap.9	unk	unk	0,1,1,1,1,0,2,
585	CM002910-snap.10	CM002910	-	101745	105270	101745	105270	4	101745,103698,103802,105263,	102135,103746,104269,105270,	gene.CM002910-snap.10	unk	unk	0,0,1,0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

SNAP Genes (BUSCO) (snapBUSCO) Track Description


	Description This track shows the gene predictions from the SNAP gene finder using the species-specific parameters estimated from a training set produced by BUSCO. Methods The training set used to estimate the species-specific parameters for the SNAP analysis was produced by BUSCO using the arthropoda_odb9 dataset. References Korf I. Gene finding in novel genomes. BMC Bioinformatics. 2004 May 14;5:59. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015 Oct 1;31(19):3210-2.

Description