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

Database: DvirCAF1 Primary Table: snapBUSCO Row Count: 14,745 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_10024-snap.1	`varchar(255)`	values
`chrom`	scaffold_10024	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	301	`int(10) unsigned`	range
`txEnd`	4595	`int(10) unsigned`	range
`cdsStart`	301	`int(10) unsigned`	range
`cdsEnd`	4595	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	301,2811,	`longblob`
`exonEnds`	1447,4595,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.scaffold_10024-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,1,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	scaffold_10024-snap.1	scaffold_10024	+	301	4595	301	4595	2	301,2811,	1447,4595,	gene.scaffold_10024-snap.1	unk	unk	1,1,
585	scaffold_10051-snap.1	scaffold_10051	-	50	864	50	864	2	50,576,	478,864,	gene.scaffold_10051-snap.1	unk	unk	1,1,
585	scaffold_10055-snap.1	scaffold_10055	+	704	1272	704	1272	2	704,1236,	946,1272,	gene.scaffold_10055-snap.1	unk	unk	1,0,
585	scaffold_10060-snap.1	scaffold_10060	+	56	805	56	805	1	56,	805,	gene.scaffold_10060-snap.1	unk	unk	1,
585	scaffold_10191-snap.1	scaffold_10191	+	21	573	21	573	2	21,491,	386,573,	gene.scaffold_10191-snap.1	unk	unk	0,2,
585	scaffold_10248-snap.1	scaffold_10248	+	500	1538	500	1538	2	500,1510,	850,1538,	gene.scaffold_10248-snap.1	unk	unk	0,2,
585	scaffold_10311-snap.1	scaffold_10311	-	1631	2108	1631	2108	2	1631,2102,	1832,2108,	gene.scaffold_10311-snap.1	unk	unk	0,0,
585	scaffold_10322-snap.1	scaffold_10322	+	51315	58668	51315	58668	6	51315,53242,53452,57909,58224,58359,	51322,53396,53601,58058,58266,58668,	gene.scaffold_10322-snap.1	unk	unk	0,1,2,1,0,0,
585	scaffold_10322-snap.2	scaffold_10322	-	53309	57533	53309	57533	2	53309,57524,	53495,57533,	gene.scaffold_10322-snap.2	unk	unk	0,0,
585	scaffold_10322-snap.3	scaffold_10322	-	59026	62132	59026	62132	4	59026,59213,61397,62128,	59108,61330,61519,62132,	gene.scaffold_10322-snap.3	unk	unk	2,0,1,0,

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