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

Database: DgriCAF1 Primary Table: snapBUSCO Row Count: 17,182 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_10012-snap.1	`varchar(255)`	values
`chrom`	scaffold_10012	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	64	`int(10) unsigned`	range
`txEnd`	891	`int(10) unsigned`	range
`cdsStart`	64	`int(10) unsigned`	range
`cdsEnd`	891	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	64,801,	`longblob`
`exonEnds`	441,891,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.scaffold_10012-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	scaffold_10012-snap.1	scaffold_10012	+	64	891	64	891	2	64,801,	441,891,	gene.scaffold_10012-snap.1	unk	unk	1,0,
585	scaffold_10016-snap.1	scaffold_10016	+	62	385	62	385	2	62,240,	178,385,	gene.scaffold_10016-snap.1	unk	unk	0,2,
585	scaffold_10024-snap.1	scaffold_10024	+	852	1320	852	1320	2	852,1086,	1034,1320,	gene.scaffold_10024-snap.1	unk	unk	2,1,
585	scaffold_10027-snap.1	scaffold_10027	+	152	969	152	969	5	152,485,625,806,949,	421,560,725,894,969,	gene.scaffold_10027-snap.1	unk	unk	0,2,2,0,1,
585	scaffold_10030-snap.1	scaffold_10030	-	475	1182	475	1182	4	475,557,851,1175,	503,610,1003,1182,	gene.scaffold_10030-snap.1	unk	unk	2,0,1,0,
585	scaffold_10030-snap.2	scaffold_10030	+	17042	22373	17042	22373	3	17042,21755,22255,	17051,21913,22373,	gene.scaffold_10030-snap.2	unk	unk	0,0,2,
585	scaffold_10032-snap.1	scaffold_10032	+	158	1066	158	1066	1	158,	1066,	gene.scaffold_10032-snap.1	unk	unk	1,
585	scaffold_10033-snap.1	scaffold_10033	+	425	1783	425	1783	2	425,1460,	876,1783,	gene.scaffold_10033-snap.1	unk	unk	0,1,
585	scaffold_10058-snap.1	scaffold_10058	+	166	728	166	728	2	166,611,	470,728,	gene.scaffold_10058-snap.1	unk	unk	2,0,
585	scaffold_10059-snap.1	scaffold_10059	-	157	1943	157	1943	3	157,1474,1685,	217,1621,1943,	gene.scaffold_10059-snap.1	unk	unk	0,0,0,

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