Schema for GeMoMa Genes - GeMoMa Gene Predictions

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Schema for GeMoMa Genes - GeMoMa Gene Predictions

Database: DyakCAF1 Primary Table: GeMoMa Row Count: 13,778 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	FBTR0078170_R0	`varchar(255)`	values
`chrom`	chr2L	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	8643	`int(10) unsigned`	range
`txEnd`	14684	`int(10) unsigned`	range
`cdsStart`	8643	`int(10) unsigned`	range
`cdsEnd`	14684	`int(10) unsigned`	range
`exonCount`	8	`int(10) unsigned`	range
`exonStarts`	8643,8836,9279,9784,10693,1...	`longblob`
`exonEnds`	8773,8945,9722,10427,10799,...	`longblob`
`score`	0	`int(11)`	range
`name2`	gene_1309	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	2,1,2,1,0,2,0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	FBTR0078170_R0	chr2L	-	8643	14684	8643	14684	8	8643,8836,9279,9784,10693,10856,12106,14600,	8773,8945,9722,10427,10799,12048,12885,14684,	0	gene_1309	unk	unk	2,1,2,1,0,2,0,0,
585	FBTR0113008_R0	chr2L	-	16689	19686	16689	19686	5	16689,17518,17769,18715,19281,	17455,17711,18649,18997,19686,	0	gene_1310	unk	unk	2,1,0,0,0,
585	FBTR0309229_R0	chr2L	-	20962	34453	20962	34453	14	20962,21194,21490,22503,23238,23487,27371,28097,28211,29220,29841,32040,32502,34398,	21130,21393,21928,22729,23432,23574,27815,28144,28695,29756,31795,32237,33059,34453,	0	gene_1311	unk	unk	0,2,2,1,2,2,2,0,2,0,2,0,1,0,
585	FBTR0078100_R0	chr2L	+	56139	59389	56139	59389	4	56139,56413,56602,59103,	56277,56545,59046,59389,	0	gene_0	unk	unk	0,0,0,2,
585	FBTR0078101_R0	chr2L	+	61801	65401	61801	65401	3	61801,64196,64380,	62173,64312,65401,	0	gene_1	unk	unk	0,0,2,
585	FBTR0306541_R0	chr2L	+	65733	66997	65733	66997	2	65733,66929,	66871,66997,	0	gene_2	unk	unk	0,1,
585	FBTR0290323_R0	chr2L	-	72463	76384	72463	76384	2	72463,76311,	73485,76384,	0	gene_1312	unk	unk	1,0,
585	FBTR0078103_R0	chr2L	+	84208	91342	84208	91342	12	84208,84337,84480,84698,87227,87873,89130,89917,90107,90361,90594,91299,	84249,84419,84650,87178,87814,89070,89862,90049,90288,90540,90965,91342,	0	gene_3	unk	unk	0,2,0,2,1,0,0,0,0,1,0,2,
585	FBTR0078104_R0	chr2L	+	91798	93127	91798	93127	3	91798,92369,92879,	92246,92798,93127,	0	gene_4	unk	unk	0,1,1,
585	FBTR0301452_R0	chr2L	-	93839	96016	93839	96016	5	93839,94370,94760,94881,95342,	94314,94702,94825,95285,96016,	0	gene_1313	unk	unk	2,0,1,2,0,

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. yakuba (DyakCAF1) assembly and the predicted gene models were constructed using GeMoMa. Methods D. melanogaster protein sequences were aligned against the D. yakuba (DyakCAF1) 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.