Schema for GeMoMa Genes - GeMoMa Gene Predictions

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Schema for GeMoMa Genes - GeMoMa Gene Predictions

Database: DtakGB2 Primary Table: GeMoMa Row Count: 13,394 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	FBTR0086083_R0	`varchar(255)`	values
`chrom`	AFFI02000003	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	10545	`int(10) unsigned`	range
`txEnd`	32417	`int(10) unsigned`	range
`cdsStart`	10545	`int(10) unsigned`	range
`cdsEnd`	32417	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	10545,31969,	`longblob`
`exonEnds`	11330,32417,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene_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	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	FBTR0086083_R0	AFFI02000003	-	10545	32417	10545	32417	2	10545,31969,	11330,32417,	0	gene_1	unk	unk	1,0,
585	FBTR0086077_R0	AFFI02000003	+	39357	42477	39357	42477	2	39357,39950,	39896,42477,	0	gene_0	unk	unk	0,2,
585	FBTR0082757_R0	AFFI02000009	+	10234	12297	10234	12297	2	10234,11516,	11046,12297,	0	gene_2	unk	unk	0,2,
585	FBTR0082759_R0	AFFI02000009	+	17689	19534	17689	19534	3	17689,18383,19046,	18043,18780,19534,	0	gene_3	unk	unk	0,0,1,
585	FBTR0100020_R0	AFFI02000009	+	19833	20195	19833	20195	2	19833,20060,	19983,20195,	0	gene_4	unk	unk	0,0,
585	FBTR0082760_R0	AFFI02000009	+	21249	25481	21249	25481	4	21249,24069,24284,25295,	21321,24204,24644,25481,	0	gene_5	unk	unk	0,0,0,0,
585	FBTR0082756_R1	AFFI02000009	-	26034	26334	26034	26334	1	26034,	26334,	0	gene_7	unk	unk	0,
585	FBTR0344428_R0	AFFI02000009	+	26278	27467	26278	27467	2	26278,27128,	26356,27467,	0	gene_6	unk	unk	0,0,
585	FBTR0078587_R0	AFFI02000021	-	5215	8363	5215	8363	5	5215,6380,6947,7456,8152,	6318,6533,7367,7795,8363,	0	gene_9	unk	unk	1,1,1,1,0,
585	FBTR0078616_R0	AFFI02000021	+	10218	16399	10218	16399	2	10218,15925,	11106,16399,	0	gene_8	unk	unk	0,0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

GeMoMa Genes (GeMoMa) Track Description


	Description D. melanogaster protein sequences from FlyBase were aligned against each scaffold in the D. takahashii (DtakGB2) assembly and the predicted gene models were constructed using GeMoMa. Methods D. melanogaster protein sequences were aligned against the D. takahashii (DtakGB2) genome assembly using NCBI TBLASTN with the following parameters: -evalue 1e-5 -max_intron_length 100000 -matrix BLOSUM80 -gapopen 13 -gapextend 2 -soft_masking true -db_soft_mask 30 -best_hit_overhang 0.1 -best_hit_score_edge 0.1 The TBLASTN results were used by GeMoMa to produce an initial set of gene predictions. The GeMoMa predictions are then filtered by the `GAF` module in GeMoMa to produce the final set of gene predictions. References Keilwagen J, Wenk M, Erickson JL, Schattat MH, Grau J, Hartung F. Using intron position conservation for homology-based gene prediction. Nucleic Acids Res. 2016 May 19;44(9):e89.