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

Database: DanaCAF1 Primary Table: snapBUSCO Row Count: 13,437 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_0-snap.1	`varchar(255)`	values
`chrom`	scaffold_0	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	33	`int(10) unsigned`	range
`txEnd`	334	`int(10) unsigned`	range
`cdsStart`	33	`int(10) unsigned`	range
`cdsEnd`	334	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	33,157,	`longblob`
`exonEnds`	96,334,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.scaffold_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,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	scaffold_0-snap.1	scaffold_0	+	33	334	33	334	2	33,157,	96,334,	gene.scaffold_0-snap.1	unk	unk	0,0,
585	scaffold_10217-snap.1	scaffold_10217	-	7019	7588	7019	7588	2	7019,7582,	7304,7588,	gene.scaffold_10217-snap.1	unk	unk	0,0,
585	scaffold_10296-snap.1	scaffold_10296	+	260	1246	260	1246	2	260,970,	590,1246,	gene.scaffold_10296-snap.1	unk	unk	1,1,
585	scaffold_10492-snap.1	scaffold_10492	+	58	518	58	518	2	58,341,	191,518,	gene.scaffold_10492-snap.1	unk	unk	2,0,
585	scaffold_10550-snap.1	scaffold_10550	+	181	993	181	993	1	181,	993,	gene.scaffold_10550-snap.1	unk	unk	0,
585	scaffold_10575-snap.1	scaffold_10575	-	128	2729	128	2729	5	128,401,726,1159,2723,	345,664,1062,1792,2729,	gene.scaffold_10575-snap.1	unk	unk	2,0,0,0,0,
585	scaffold_10575-snap.2	scaffold_10575	-	3178	5723	3178	5723	3	3178,4766,5716,	3190,5095,5723,	gene.scaffold_10575-snap.2	unk	unk	0,1,0,
585	scaffold_11114-snap.1	scaffold_11114	+	25	966	25	966	1	25,	966,	gene.scaffold_11114-snap.1	unk	unk	1,
585	scaffold_11116-snap.1	scaffold_11116	+	365	1207	365	1207	1	365,	1207,	gene.scaffold_11116-snap.1	unk	unk	1,
585	scaffold_11175-snap.1	scaffold_11175	+	421	936	421	936	1	421,	936,	gene.scaffold_11175-snap.1	unk	unk	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