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

Database: DperCAF1 Primary Table: snapBUSCO Row Count: 16,630 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	super_0-snap.1	`varchar(255)`	values
`chrom`	super_0	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	4561	`int(10) unsigned`	range
`txEnd`	7429	`int(10) unsigned`	range
`cdsStart`	4561	`int(10) unsigned`	range
`cdsEnd`	7429	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	4561,5089,7398,	`longblob`
`exonEnds`	4567,5262,7429,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.super_0-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,0,2,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	super_0-snap.1	super_0	+	4561	7429	4561	7429	3	4561,5089,7398,	4567,5262,7429,	gene.super_0-snap.1	unk	unk	0,0,2,
585	super_0-snap.2	super_0	+	30374	32191	30374	32191	3	30374,31727,32065,	30383,32006,32191,	gene.super_0-snap.2	unk	unk	0,0,0,
585	super_0-snap.3	super_0	+	34022	37410	34022	37410	9	34022,35316,35756,35939,36164,36579,36704,36951,37193,	34028,35696,35915,36072,36575,36650,36927,37043,37410,	gene.super_0-snap.3	unk	unk	0,0,2,2,0,0,2,0,2,
585	super_0-snap.4	super_0	-	34257	40701	34257	40701	9	34257,34853,35301,37526,38231,38485,38912,39697,40694,	34270,35204,37325,37803,38427,38570,39271,40021,40701,	gene.super_0-snap.4	unk	unk	2,2,0,2,1,0,1,1,0,
585	super_0-snap.5	super_0	-	44718	56669	44718	56669	4	44718,53838,54680,56660,	44788,54646,55194,56669,	gene.super_0-snap.5	unk	unk	2,1,0,0,
585	super_0-snap.6	super_0	+	48841	54627	48841	54627	5	48841,53397,53856,54044,54429,	48849,53453,54014,54419,54627,	gene.super_0-snap.6	unk	unk	0,2,1,0,0,
585	super_0-snap.7	super_0	+	57387	62149	57387	62149	3	57387,59625,61860,	57394,59659,62149,	gene.super_0-snap.7	unk	unk	0,1,2,
585	super_0-snap.8	super_0	-	57472	65747	57472	65747	6	57472,61214,63736,64202,64720,65537,	57517,61223,64198,64642,65453,65747,	gene.super_0-snap.8	unk	unk	0,0,0,1,0,0,
585	super_0-snap.9	super_0	+	63101	72022	63101	72022	6	63101,63635,63928,66008,69475,71859,	63105,63912,65698,68024,71746,72022,	gene.super_0-snap.9	unk	unk	0,1,2,2,2,2,
585	super_0-snap.10	super_0	+	73733	80801	73733	80801	2	73733,79701,	73740,80801,	gene.super_0-snap.10	unk	unk	0,1,

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

Methods

References