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

Database: DpseGB3 Primary Table: snapBUSCO Row Count: 21,081 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	CH379058-snap.1	`varchar(255)`	values
`chrom`	CH379058	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	130	`int(10) unsigned`	range
`txEnd`	557	`int(10) unsigned`	range
`cdsStart`	130	`int(10) unsigned`	range
`cdsEnd`	557	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	130,541,	`longblob`
`exonEnds`	477,557,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.CH379058-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	CH379058-snap.1	CH379058	-	130	557	130	557	2	130,541,	477,557,	gene.CH379058-snap.1	unk	unk	1,0,
585	CH379058-snap.2	CH379058	+	2856	3848	2856	3848	2	2856,3734,	3006,3848,	gene.CH379058-snap.2	unk	unk	0,0,
585	CH379058-snap.3	CH379058	+	8113	12490	8113	12490	3	8113,10191,12414,	8217,10236,12490,	gene.CH379058-snap.3	unk	unk	0,2,2,
585	CH379058-snap.4	CH379058	-	13994	25112	13994	25112	6	13994,15201,17139,24521,24712,25087,	14003,15226,22629,24598,24774,25112,	gene.CH379058-snap.4	unk	unk	0,2,2,0,1,0,
585	CH379058-snap.5	CH379058	+	22002	25508	22002	25508	2	22002,25378,	22400,25508,	gene.CH379058-snap.5	unk	unk	0,2,
585	CH379058-snap.6	CH379058	-	26783	27497	26783	27497	2	26783,27440,	26939,27497,	gene.CH379058-snap.6	unk	unk	0,0,
585	CH379058-snap.7	CH379058	-	32479	34764	32479	34764	3	32479,33273,34746,	32632,33285,34764,	gene.CH379058-snap.7	unk	unk	0,0,0,
585	CH379058-snap.8	CH379058	-	35933	41567	35933	41567	3	35933,40573,41517,	35969,40709,41567,	gene.CH379058-snap.8	unk	unk	0,2,0,
585	CH379058-snap.9	CH379058	-	43169	43998	43169	43998	2	43169,43865,	43333,43998,	gene.CH379058-snap.9	unk	unk	1,0,
585	CH379058-snap.10	CH379058	+	45684	45945	45684	45945	2	45684,45839,	45770,45945,	gene.CH379058-snap.10	unk	unk	0,2,

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