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

Database: DereCAF1 Primary Table: snapBUSCO Row Count: 12,391 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_1230-snap.1	`varchar(255)`	values
`chrom`	scaffold_1230	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	246	`int(10) unsigned`	range
`txEnd`	972	`int(10) unsigned`	range
`cdsStart`	246	`int(10) unsigned`	range
`cdsEnd`	972	`int(10) unsigned`	range
`exonCount`	4	`int(10) unsigned`	range
`exonStarts`	246,423,741,886,	`longblob`
`exonEnds`	367,667,832,972,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.scaffold_1230-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	2,1,0,1,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	scaffold_1230-snap.1	scaffold_1230	-	246	972	246	972	4	246,423,741,886,	367,667,832,972,	gene.scaffold_1230-snap.1	unk	unk	2,1,0,1,
585	scaffold_1240-snap.1	scaffold_1240	-	388	1382	388	1382	1	388,	1382,	gene.scaffold_1240-snap.1	unk	unk	2,
585	scaffold_1245-snap.1	scaffold_1245	-	191	1156	191	1156	1	191,	1156,	gene.scaffold_1245-snap.1	unk	unk	1,
585	scaffold_1246-snap.1	scaffold_1246	+	30	1113	30	1113	2	30,330,	36,1113,	gene.scaffold_1246-snap.1	unk	unk	0,0,
585	scaffold_1247-snap.1	scaffold_1247	-	244	1170	244	1170	1	244,	1170,	gene.scaffold_1247-snap.1	unk	unk	1,
585	scaffold_1251-snap.1	scaffold_1251	+	314	1475	314	1475	3	314,773,1217,	320,1136,1475,	gene.scaffold_1251-snap.1	unk	unk	0,0,0,
585	scaffold_1252-snap.1	scaffold_1252	-	107	888	107	888	2	107,697,	616,888,	gene.scaffold_1252-snap.1	unk	unk	0,1,
585	scaffold_1253-snap.1	scaffold_1253	-	299	1874	299	1874	3	299,486,1724,	405,1328,1874,	gene.scaffold_1253-snap.1	unk	unk	0,1,1,
585	scaffold_1255-snap.1	scaffold_1255	+	80	900	80	900	2	80,426,	322,900,	gene.scaffold_1255-snap.1	unk	unk	1,0,
585	scaffold_1259-snap.1	scaffold_1259	-	133	1270	133	1270	2	133,993,	220,1270,	gene.scaffold_1259-snap.1	unk	unk	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