Schema for GeMoMa Genes - GeMoMa Gene Predictions

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Schema for GeMoMa Genes - GeMoMa Gene Predictions

Database: DpseGB3 Primary Table: GeMoMa Row Count: 12,238 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	FBTR0079202_R0	`varchar(255)`	values
`chrom`	CH379058	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	17120	`int(10) unsigned`	range
`txEnd`	22628	`int(10) unsigned`	range
`cdsStart`	17120	`int(10) unsigned`	range
`cdsEnd`	22628	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	17120,	`longblob`
`exonEnds`	22628,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene_216	`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	FBTR0079202_R0	CH379058	-	17120	22628	17120	22628	1	17120,	22628,	0	gene_216	unk	unk	0,
585	FBTR0091802_R6	CH379058	-	26783	27607	26783	27607	4	26783,27000,27230,27595,	26939,27168,27383,27607,	0	gene_217	unk	unk	0,0,0,0,
585	FBTR0079201_R0	CH379058	+	57285	58473	57285	58473	4	57285,57379,57841,58214,	57325,57776,58099,58473,	0	gene_0	unk	unk	0,1,2,2,
585	FBTR0303078_R0	CH379058	+	58811	59477	58811	59477	3	58811,58972,59383,	58899,59324,59477,	0	gene_1	unk	unk	0,1,2,
585	FBTR0303079_R0	CH379058	+	59479	61516	59479	61516	1	59479,	61516,	0	gene_2	unk	unk	0,
585	FBTR0299947_R0	CH379058	-	61562	64766	61562	64766	1	61562,	64766,	0	gene_218	unk	unk	0,
585	FBTR0333407_R0	CH379058	+	68527	70371	68527	70371	4	68527,68601,69530,69748,	68537,69475,69718,70371,	0	gene_3	unk	unk	0,1,2,1,
585	FBTR0079200_R0	CH379058	-	70546	71053	70546	71053	1	70546,	71053,	0	gene_219	unk	unk	0,
585	FBTR0304908_R0	CH379058	-	74330	78590	74330	78590	6	74330,74559,75375,75584,75859,78184,	74417,74715,75522,75770,76029,78590,	0	gene_220	unk	unk	0,0,0,0,1,0,
586	FBTR0079211_R0	CH379058	+	150786	152307	150786	152307	4	150786,150987,151990,152221,	150927,151929,152153,152307,	0	gene_4	unk	unk	0,0,0,1,

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. pseudoobscura (DpseGB3) assembly and the predicted gene models were constructed using GeMoMa. Methods D. melanogaster protein sequences were aligned against the D. pseudoobscura (DpseGB3) 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.