Schema for GeMoMa Genes - GeMoMa Gene Predictions

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Schema for GeMoMa Genes - GeMoMa Gene Predictions

Database: DhydGB1 Primary Table: GeMoMa Row Count: 11,329 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	FBTR0307895_R0	`varchar(255)`	values
`chrom`	NWQH01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	25096	`int(10) unsigned`	range
`txEnd`	32312	`int(10) unsigned`	range
`cdsStart`	25096	`int(10) unsigned`	range
`cdsEnd`	32312	`int(10) unsigned`	range
`exonCount`	11	`int(10) unsigned`	range
`exonStarts`	25096,25277,25485,26820,278...	`longblob`
`exonEnds`	25132,25365,25634,27118,279...	`longblob`
`score`	0	`int(11)`	range
`name2`	gene_0	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,0,1,0,1,1,0,1,2,0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	FBTR0307895_R0	NWQH01000001	+	25096	32312	25096	32312	11	25096,25277,25485,26820,27805,28045,28584,29834,31514,31673,32213,	25132,25365,25634,27118,27988,28326,28735,30000,31614,32153,32312,	0	gene_0	unk	unk	0,0,1,0,1,1,0,1,2,0,0,
585	FBTR0077609_R0	NWQH01000001	-	38662	43116	38662	43116	6	38662,39239,40325,40605,40856,43006,	39180,40217,40543,40758,41318,43116,	0	gene_126	unk	unk	1,1,2,2,2,0,
585	FBTR0081916_R0	NWQH01000001	-	73243	74676	73243	74676	4	73243,73664,73907,74238,	73600,73850,74177,74676,	0	gene_127	unk	unk	0,0,0,0,
585	FBTR0070277_R0	NWQH01000001	+	97964	102410	97964	102410	5	97964,98511,99458,101979,102221,	98438,98632,99720,102103,102410,	0	gene_1	unk	unk	0,0,1,2,0,
586	FBTR0070279_R0	NWQH01000001	+	151250	152567	151250	152567	1	151250,	152567,	0	gene_2	unk	unk	0,
586	FBTR0089815_R0	NWQH01000001	+	155217	177898	155217	177898	15	155217,155655,155777,155978,164199,165479,165974,167383,167896,168025,168440,168942,169472,169938,176824,	155323,155709,155920,156587,164290,165594,166073,167547,167962,168109,168503,169405,169655,170032,177898,	0	gene_3	unk	unk	0,1,1,0,0,1,2,2,1,1,1,1,2,2,0,
586	FBTR0070272_R0	NWQH01000001	-	157128	161334	157128	161334	5	157128,157884,158646,158853,160814,	157815,158106,158767,158947,161334,	0	gene_128	unk	unk	0,0,2,1,0,
586	FBTR0273400_R0	NWQH01000001	-	166058	166793	166058	166793	3	166058,166513,166777,	166458,166703,166793,	0	gene_129	unk	unk	2,1,0,
586	FBTR0070270_R0	NWQH01000001	-	181289	183211	181289	183211	4	181289,181745,182321,183199,	181682,182256,183151,183211,	0	gene_130	unk	unk	0,2,0,0,
586	FBTR0070283_R0	NWQH01000001	+	185489	185971	185489	185971	2	185489,185750,	185691,185971,	0	gene_4	unk	unk	0,1,

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. hydei (DhydGB1) assembly and the predicted gene models were constructed using GeMoMa. Methods D. melanogaster protein sequences were aligned against the D. hydei (DhydGB1) 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.