Schema for Geneid Genes - Geneid Gene Predictions

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Schema for Geneid Genes - Geneid Gene Predictions

Database: DyakCAF1 Primary Table: geneid Row Count: 18,828 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	mRNA_geneid-chr2L_1	`varchar(255)`	values
`chrom`	chr2L	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	4506	`int(10) unsigned`	range
`txEnd`	11258	`int(10) unsigned`	range
`cdsStart`	4506	`int(10) unsigned`	range
`cdsEnd`	11258	`int(10) unsigned`	range
`exonCount`	5	`int(10) unsigned`	range
`exonStarts`	4506,9279,9784,10693,10856,	`longblob`
`exonEnds`	4514,9722,10349,10799,11258,	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid-chr2L_1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,2,1,0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	mRNA_geneid-chr2L_1	chr2L	-	4506	11258	4506	11258	5	4506,9279,9784,10693,10856,	4514,9722,10349,10799,11258,	0	geneid-chr2L_1	unk	unk	1,2,1,0,0,
585	mRNA_geneid-chr2L_2	chr2L	-	16689	28772	16689	28772	12	16689,17541,17769,18264,21194,21490,22503,23238,24943,27559,28097,28211,	17214,17711,17865,18649,21393,21928,22700,23323,25710,27815,28144,28772,	0	geneid-chr2L_2	unk	unk	0,1,1,0,2,2,0,2,0,2,0,0,
585	mRNA_geneid-chr2L_3	chr2L	-	29805	47705	29805	47705	4	29805,32040,32502,47635,	31795,32237,33059,47705,	0	geneid-chr2L_3	unk	unk	2,0,1,0,
585	mRNA_geneid-chr2L_4	chr2L	+	56139	59389	56139	59389	3	56139,56602,59103,	56277,59046,59389,	0	geneid-chr2L_4	unk	unk	0,0,2,
585	mRNA_geneid-chr2L_5	chr2L	+	61801	67377	61801	67377	5	61801,62894,64196,64380,67131,	62173,63086,64312,64669,67377,	0	geneid-chr2L_5	unk	unk	0,0,0,2,0,
585	mRNA_geneid-chr2L_6	chr2L	-	72463	80745	72463	80745	2	72463,80732,	73485,80745,	0	geneid-chr2L_6	unk	unk	1,0,
585	mRNA_geneid-chr2L_7	chr2L	+	84208	93305	84208	93305	8	84208,84788,88114,90594,90940,91893,92369,93246,	84249,85732,88338,90724,90965,92246,92798,93305,	0	geneid-chr2L_7	unk	unk	0,2,1,0,1,2,1,1,
585	mRNA_geneid-chr2L_8	chr2L	-	93839	94268	93839	94268	1	93839,	94268,	0	geneid-chr2L_8	unk	unk	0,
585	mRNA_geneid-chr2L_9	chr2L	-	95302	96016	95302	96016	1	95302,	96016,	0	geneid-chr2L_9	unk	unk	0,
585	mRNA_geneid-chr2L_10	chr2L	+	98063	102729	98063	102729	6	98063,99782,99927,100177,101876,102620,	98187,99860,100050,100347,102556,102729,	0	geneid-chr2L_10	unk	unk	0,1,1,1,0,2,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Geneid Genes (geneid) Track Description


	Description This track shows gene predictions from the geneid program developed by Roderic Guigó's Computational Biology of RNA Processing group which is part of the Centre de Regulació Genòmica (CRG) in Barcelona, Catalunya, Spain. Methods Geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. Credits Thanks to Computational Biology of RNA Processing for providing these data. References Blanco E, Parra G, Guigó R. Using geneid to identify genes. Curr Protoc Bioinformatics. 2007 Jun;Chapter 4:Unit 4.3. PMID: 18428791 Parra G, Blanco E, Guigó R. GeneID in Drosophila. Genome Res. 2000 Apr;10(4):511-5. PMID: 10779490; PMC: PMC310871