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

Database: DmirGB2 Primary Table: snapBUSCO Row Count: 16,710 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	CM001516-snap.1	`varchar(255)`	values
`chrom`	CM001516	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	1943	`int(10) unsigned`	range
`txEnd`	2232	`int(10) unsigned`	range
`cdsStart`	1943	`int(10) unsigned`	range
`cdsEnd`	2232	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	1943,2181,	`longblob`
`exonEnds`	2138,2232,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.CM001516-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	CM001516-snap.1	CM001516	-	1943	2232	1943	2232	2	1943,2181,	2138,2232,	gene.CM001516-snap.1	unk	unk	0,0,
585	CM001516-snap.2	CM001516	-	4412	4772	4412	4772	2	4412,4766,	4721,4772,	gene.CM001516-snap.2	unk	unk	0,0,
585	CM001516-snap.3	CM001516	+	15164	18026	15164	18026	6	15164,15381,16029,16218,16356,16925,	15315,15755,16158,16324,16742,18026,	gene.CM001516-snap.3	unk	unk	0,1,0,0,1,0,
585	CM001516-snap.4	CM001516	+	18571	21013	18571	21013	5	18571,18878,19130,19783,20817,	18644,19050,19763,20737,21013,	gene.CM001516-snap.4	unk	unk	0,1,2,2,2,
585	CM001516-snap.5	CM001516	+	22577	29360	22577	29360	11	22577,22594,23254,23462,24309,24698,25430,25969,26350,26512,29252,	22583,22767,23405,24243,24596,25178,25922,26296,26439,28247,29360,	gene.CM001516-snap.5	unk	unk	0,0,2,0,1,0,0,0,0,2,0,
585	CM001516-snap.6	CM001516	-	30530	33848	30530	33848	4	30530,31094,31826,33842,	31017,31757,32365,33848,	gene.CM001516-snap.6	unk	unk	2,2,0,0,
585	CM001516-snap.7	CM001516	-	37144	43341	37144	43341	4	37144,42295,42560,43337,	37225,42347,43275,43341,	gene.CM001516-snap.7	unk	unk	0,2,1,0,
585	CM001516-snap.8	CM001516	+	39943	44350	39943	44350	4	39943,41776,42274,42504,	39949,41886,42415,44350,	gene.CM001516-snap.8	unk	unk	0,0,2,2,
585	CM001516-snap.9	CM001516	+	45479	46843	45479	46843	4	45479,45701,46263,46539,	45488,45711,46465,46843,	gene.CM001516-snap.9	unk	unk	0,0,1,2,
585	CM001516-snap.10	CM001516	+	48240	50124	48240	50124	2	48240,48641,	48245,50124,	gene.CM001516-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