Schema for GeMoMa Genes - GeMoMa Gene Predictions

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Schema for GeMoMa Genes - GeMoMa Gene Predictions

Database: DrhoGB2 Primary Table: GeMoMa Row Count: 13,145 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	FBTR0300458_R1	`varchar(255)`	values
`chrom`	AFPP02000044	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	554	`int(10) unsigned`	range
`txEnd`	1694	`int(10) unsigned`	range
`cdsStart`	554	`int(10) unsigned`	range
`cdsEnd`	1694	`int(10) unsigned`	range
`exonCount`	4	`int(10) unsigned`	range
`exonStarts`	554,704,1541,1662,	`longblob`
`exonEnds`	632,1110,1598,1694,	`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`	0,2,2,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	FBTR0300458_R1	AFPP02000044	-	554	1694	554	1694	4	554,704,1541,1662,	632,1110,1598,1694,	0	gene_0	unk	unk	0,2,2,0,
585	FBTR0310471_R1	AFPP02000045	-	547	757	547	757	2	547,726,	666,757,	0	gene_1	unk	unk	1,0,
585	FBTR0079601_R1	AFPP02000067	+	27	371	27	371	2	27,125,	66,371,	0	gene_2	unk	unk	0,0,
585	FBTR0079714_R0	AFPP02000123	+	286	657	286	657	2	286,361,	296,657,	0	gene_3	unk	unk	0,1,
585	FBTR0079713_R1	AFPP02000123	+	1337	2584	1337	2584	2	1337,2268,	1348,2584,	0	gene_4	unk	unk	0,2,
585	FBTR0085686_R3	AFPP02000174	+	1	846	1	846	4	1,276,512,748,	220,336,678,846,	0	gene_5	unk	unk	0,0,0,1,
585	FBTR0299995_R1	AFPP02000175	-	486	954	486	954	1	486,	954,	0	gene_6	unk	unk	0,
585	FBTR0333890_R0	AFPP02000180	-	1092	1272	1092	1272	2	1092,1251,	1188,1272,	0	gene_8	unk	unk	0,0,
585	FBTR0076571_R0	AFPP02000180	+	2348	3061	2348	3061	2	2348,2542,	2363,3061,	0	gene_7	unk	unk	0,0,
585	FBTR0076592_R0	AFPP02000184	-	5323	5608	5323	5608	1	5323,	5608,	0	gene_9	unk	unk	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. rhopaloa (DrhoGB2) assembly and the predicted gene models were constructed using GeMoMa. Methods D. melanogaster protein sequences were aligned against the D. rhopaloa (DrhoGB2) 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.