Schema for Geneid Genes - Geneid Gene Predictions

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Schema for Geneid Genes - Geneid Gene Predictions

Database: DereCAF1 Primary Table: geneid Row Count: 16,234 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	mRNA_geneid-scaffold_1000_1	`varchar(255)`	values
`chrom`	scaffold_1000	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	12	`int(10) unsigned`	range
`txEnd`	18	`int(10) unsigned`	range
`cdsStart`	12	`int(10) unsigned`	range
`cdsEnd`	18	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	12,	`longblob`
`exonEnds`	18,	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid-scaffold_1000_1	`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	mRNA_geneid-scaffold_1000_1	scaffold_1000	+	12	18	12	18	1	12,	18,	0	geneid-scaffold_1000_1	unk	unk	0,
585	mRNA_geneid-scaffold_1007_1	scaffold_1007	-	810	816	810	816	1	810,	816,	0	geneid-scaffold_1007_1	unk	unk	0,
585	mRNA_geneid-scaffold_1009_1	scaffold_1009	-	237	252	237	252	1	237,	252,	0	geneid-scaffold_1009_1	unk	unk	0,
585	mRNA_geneid-scaffold_1010_1	scaffold_1010	+	1975	1987	1975	1987	1	1975,	1987,	0	geneid-scaffold_1010_1	unk	unk	0,
585	mRNA_geneid-scaffold_1012_1	scaffold_1012	+	1338	1341	1338	1341	1	1338,	1341,	0	geneid-scaffold_1012_1	unk	unk	0,
585	mRNA_geneid-scaffold_102_1	scaffold_102	-	2377	2383	2377	2383	1	2377,	2383,	0	geneid-scaffold_102_1	unk	unk	0,
585	mRNA_geneid-scaffold_1023_1	scaffold_1023	+	1265	1268	1265	1268	1	1265,	1268,	0	geneid-scaffold_1023_1	unk	unk	0,
585	mRNA_geneid-scaffold_1029_1	scaffold_1029	-	24	51	24	51	1	24,	51,	0	geneid-scaffold_1029_1	unk	unk	0,
585	mRNA_geneid-scaffold_103_1	scaffold_103	-	1733	1745	1733	1745	1	1733,	1745,	0	geneid-scaffold_103_1	unk	unk	0,
585	mRNA_geneid-scaffold_1035_1	scaffold_1035	+	1027	1057	1027	1057	1	1027,	1057,	0	geneid-scaffold_1035_1	unk	unk	0,

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