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

Database: DobsGB1 Primary Table: snapBUSCO Row Count: 18,290 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	BDQP01000001-snap.1	`varchar(255)`	values
`chrom`	BDQP01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	2439	`int(10) unsigned`	range
`txEnd`	7716	`int(10) unsigned`	range
`cdsStart`	2439	`int(10) unsigned`	range
`cdsEnd`	7716	`int(10) unsigned`	range
`exonCount`	4	`int(10) unsigned`	range
`exonStarts`	2439,5446,5933,7707,	`longblob`
`exonEnds`	2445,5486,6058,7716,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.BDQP01000001-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,0,1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	BDQP01000001-snap.1	BDQP01000001	+	2439	7716	2439	7716	4	2439,5446,5933,7707,	2445,5486,6058,7716,	gene.BDQP01000001-snap.1	unk	unk	0,0,1,0,
585	BDQP01000001-snap.2	BDQP01000001	+	17424	20302	17424	20302	4	17424,18205,18970,20245,	17433,18323,19158,20302,	gene.BDQP01000001-snap.2	unk	unk	0,0,1,0,
585	BDQP01000001-snap.3	BDQP01000001	+	21838	29439	21838	29439	8	21838,23291,23671,25913,26185,26487,27912,29149,	21847,23346,23987,26047,26361,26722,28683,29439,	gene.BDQP01000001-snap.3	unk	unk	0,0,1,2,1,0,1,1,
585	BDQP01000001-snap.4	BDQP01000001	+	29940	32204	29940	32204	4	29940,30315,30773,31448,	29947,30687,31387,32204,	gene.BDQP01000001-snap.4	unk	unk	0,1,1,0,
585	BDQP01000001-snap.5	BDQP01000001	-	37921	38774	37921	38774	5	37921,38186,38378,38594,38769,	38092,38315,38536,38701,38774,	gene.BDQP01000001-snap.5	unk	unk	0,0,1,2,0,
585	BDQP01000001-snap.6	BDQP01000001	-	39487	41643	39487	41643	8	39487,39863,39984,40149,40864,41134,41522,41639,	39568,39925,40091,40805,41081,41220,41569,41643,	gene.BDQP01000001-snap.6	unk	unk	0,1,2,0,2,0,1,0,
585	BDQP01000001-snap.7	BDQP01000001	+	42038	43770	42038	43770	2	42038,42829,	42042,43770,	gene.BDQP01000001-snap.7	unk	unk	0,1,
585	BDQP01000001-snap.8	BDQP01000001	-	42804	52012	42804	52012	15	42804,43483,43884,44134,46007,46501,46772,46886,47177,49733,49970,50335,50566,51679,52004,	43414,43812,44039,44232,46428,46695,46821,47100,47350,49898,50265,50488,51616,51869,52012,	gene.BDQP01000001-snap.8	unk	unk	2,0,1,2,1,2,1,0,1,1,0,0,0,2,0,
585	BDQP01000001-snap.9	BDQP01000001	+	58002	76079	58002	76079	9	58002,60764,70191,73000,73214,74288,74906,75061,75677,	58010,60792,70233,73141,73969,74594,74987,75338,76079,	gene.BDQP01000001-snap.9	unk	unk	0,2,0,0,0,2,2,2,0,
585	BDQP01000001-snap.10	BDQP01000001	+	77914	80958	77914	80958	5	77914,78108,78665,79350,79729,	77919,78594,79283,79667,80958,	gene.BDQP01000001-snap.10	unk	unk	0,2,2,2,1,

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