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

Database: DyakCAF1 Primary Table: snapBUSCO Row Count: 17,970 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	chr2L-snap.1	`varchar(255)`	values
`chrom`	chr2L	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	16689	`int(10) unsigned`	range
`txEnd`	18125	`int(10) unsigned`	range
`cdsStart`	16689	`int(10) unsigned`	range
`cdsEnd`	18125	`int(10) unsigned`	range
`exonCount`	4	`int(10) unsigned`	range
`exonStarts`	16689,17541,17769,18112,	`longblob`
`exonEnds`	17214,17711,17865,18125,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.chr2L-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,1,1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	chr2L-snap.1	chr2L	-	16689	18125	16689	18125	4	16689,17541,17769,18112,	17214,17711,17865,18125,	gene.chr2L-snap.1	unk	unk	0,1,1,0,
585	chr2L-snap.2	chr2L	-	19159	29753	19159	29753	11	19159,21194,21490,22503,23284,24171,25499,27559,28097,28211,29414,	19165,21393,21928,22700,23432,24202,25635,27815,28144,28634,29753,	gene.chr2L-snap.2	unk	unk	0,2,2,0,2,1,0,2,0,0,0,
585	chr2L-snap.3	chr2L	-	29805	37135	29805	37135	4	29805,32171,32502,37125,	31497,32237,33059,37135,	gene.chr2L-snap.3	unk	unk	0,0,1,0,
585	chr2L-snap.4	chr2L	+	57562	59050	57562	59050	2	57562,58162,	58006,59050,	gene.chr2L-snap.4	unk	unk	0,0,
585	chr2L-snap.5	chr2L	+	61265	62194	61265	62194	2	61265,61800,	61273,62194,	gene.chr2L-snap.5	unk	unk	0,2,
585	chr2L-snap.6	chr2L	+	63883	65124	63883	65124	4	63883,64196,64380,65017,	63925,64312,64883,65124,	gene.chr2L-snap.6	unk	unk	0,0,2,1,
585	chr2L-snap.7	chr2L	-	72463	75853	72463	75853	3	72463,73898,75743,	73485,73924,75853,	gene.chr2L-snap.7	unk	unk	1,2,0,
585	chr2L-snap.8	chr2L	+	84208	84666	84208	84666	2	84208,84461,	84249,84666,	gene.chr2L-snap.8	unk	unk	0,2,
585	chr2L-snap.9	chr2L	+	89604	93127	89604	93127	7	89604,90361,90594,90940,91893,92369,92879,	89650,90540,90724,90965,92246,92798,93127,	gene.chr2L-snap.9	unk	unk	0,1,0,1,2,1,1,
585	chr2L-snap.10	chr2L	-	93257	95179	93257	95179	3	93257,93923,95039,	93299,94314,95179,	gene.chr2L-snap.10	unk	unk	0,2,0,

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