Schema for GeMoMa Genes - GeMoMa Gene Predictions

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Schema for GeMoMa Genes - GeMoMa Gene Predictions

Database: DvirCAF1 Primary Table: GeMoMa Row Count: 11,603 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	FBTR0091833_R0	`varchar(255)`	values
`chrom`	scaffold_10090	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	312	`int(10) unsigned`	range
`txEnd`	687	`int(10) unsigned`	range
`cdsStart`	312	`int(10) unsigned`	range
`cdsEnd`	687	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	312,	`longblob`
`exonEnds`	687,	`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,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	FBTR0091833_R0	scaffold_10090	-	312	687	312	687	1	312,	687,	0	gene_0	unk	unk	0,
585	FBTR0088123_R6	scaffold_10273	-	1701	2136	1701	2136	1	1701,	2136,	0	gene_1	unk	unk	0,
585	FBTR0303420_R0	scaffold_10322	+	46155	54871	46155	54871	5	46155,46999,53242,53452,54767,	46195,47143,53396,53601,54871,	0	gene_2	unk	unk	0,1,1,2,1,
585	FBTR0073176_R0	scaffold_10322	+	57956	58668	57956	58668	3	57956,58224,58359,	58058,58266,58668,	0	gene_3	unk	unk	0,0,0,
585	FBTR0073160_R0	scaffold_10322	-	59209	61517	59209	61517	2	59209,61397,	61330,61517,	0	gene_27	unk	unk	0,0,
585	FBTR0073159_R0	scaffold_10322	-	62227	63856	62227	63856	5	62227,62491,62670,63414,63710,	62432,62607,62887,63642,63856,	0	gene_28	unk	unk	2,0,2,2,0,
585	FBTR0070933_R1	scaffold_10322	+	65678	67046	65678	67046	1	65678,	67046,	0	gene_5	unk	unk	0,
585	FBTR0073180_R0	scaffold_10322	+	67608	69166	67608	69166	4	67608,67750,67907,68690,	67692,67848,68632,69166,	0	gene_4	unk	unk	0,0,2,1,
585	FBTR0073158_R0	scaffold_10322	-	69287	69716	69287	69716	2	69287,69570,	69510,69716,	0	gene_29	unk	unk	2,0,
585	FBTR0072790_R0	scaffold_10322	+	72013	75597	72013	75597	2	72013,73193,	73116,75597,	0	gene_6	unk	unk	0,2,

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. virilis (DvirCAF1) assembly and the predicted gene models were constructed using GeMoMa. Methods D. melanogaster protein sequences were aligned against the D. virilis (DvirCAF1) 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.