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

Database: DserGB1 Primary Table: snapBUSCO Row Count: 16,631 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	MTTC01000001-snap.1	`varchar(255)`	values
`chrom`	MTTC01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	266	`int(10) unsigned`	range
`txEnd`	7118	`int(10) unsigned`	range
`cdsStart`	266	`int(10) unsigned`	range
`cdsEnd`	7118	`int(10) unsigned`	range
`exonCount`	4	`int(10) unsigned`	range
`exonStarts`	266,307,4722,6314,	`longblob`
`exonEnds`	270,4647,6303,7118,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.MTTC01000001-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,1,0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	MTTC01000001-snap.1	MTTC01000001	+	266	7118	266	7118	4	266,307,4722,6314,	270,4647,6303,7118,	gene.MTTC01000001-snap.1	unk	unk	0,1,0,0,
585	MTTC01000001-snap.2	MTTC01000001	+	7707	8610	7707	8610	3	7707,8057,8438,	7715,8396,8610,	gene.MTTC01000001-snap.2	unk	unk	0,2,2,
585	MTTC01000001-snap.3	MTTC01000001	+	8674	9367	8674	9367	3	8674,8694,8869,	8682,8770,9367,	gene.MTTC01000001-snap.3	unk	unk	0,2,0,
585	MTTC01000001-snap.4	MTTC01000001	+	10749	11995	10749	11995	2	10749,10973,	10756,11995,	gene.MTTC01000001-snap.4	unk	unk	0,1,
585	MTTC01000001-snap.5	MTTC01000001	+	12014	15619	12014	15619	6	12014,12503,14384,15089,15309,15601,	12018,12740,14627,15205,15561,15619,	gene.MTTC01000001-snap.5	unk	unk	0,1,1,1,0,0,
585	MTTC01000001-snap.6	MTTC01000001	+	20546	21330	20546	21330	2	20546,20826,	20552,21330,	gene.MTTC01000001-snap.6	unk	unk	0,0,
585	MTTC01000002-snap.1	MTTC01000002	+	49	2124	49	2124	5	49,212,1040,1269,1896,	147,1014,1217,1840,2124,	gene.MTTC01000002-snap.1	unk	unk	2,1,2,2,0,
585	MTTC01000002-snap.2	MTTC01000002	+	2245	2976	2245	2976	3	2245,2298,2640,	2249,2612,2976,	gene.MTTC01000002-snap.2	unk	unk	0,1,0,
585	MTTC01000002-snap.3	MTTC01000002	+	3569	5428	3569	5428	3	3569,3770,4406,	3574,4291,5428,	gene.MTTC01000002-snap.3	unk	unk	0,2,1,
585	MTTC01000002-snap.4	MTTC01000002	+	6579	16197	6579	16197	13	6579,8190,8409,8544,8678,9580,9955,10219,10961,11425,12336,12511,12941,	6587,8325,8416,8637,9542,9873,10173,10922,11417,12262,12449,12842,16197,	gene.MTTC01000002-snap.4	unk	unk	0,2,2,0,0,0,2,1,2,2,2,1,2,

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