Schema for Genscan Genes - Genscan Gene Predictions

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Schema for Genscan Genes - Genscan Gene Predictions

Database: dm3gene Primary Table: genscan Row Count: 3

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	contig1.1	`varchar(255)`	values
`chrom`	contig1	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	9	`int(10) unsigned`	range
`txEnd`	360	`int(10) unsigned`	range
`cdsStart`	9	`int(10) unsigned`	range
`cdsEnd`	360	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	9,	`longblob`
`exonEnds`	360,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	contig1.1	contig1	+	9	360	9	360	1	9,	360,
585	contig1.2	contig1	-	733	5367	733	5367	7	733,1451,2764,3400,3863,4641,5301,	1160,2705,2874,3807,4582,4814,5367,
585	contig1.3	contig1	+	5934	10570	5934	10570	4	5934,6080,6898,10145,	6019,6837,9471,10570,

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

Genscan Genes (genscan) Track Description


	Description This track shows predictions from the Genscan program written by Chris Burge. The predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The track description page offers the following filter and configuration options: Color track by codons: Select the genomic codons option to color and label each codon in a zoomed-in display to facilitate validation and comparison of gene predictions. Go to the Coloring Gene Predictions and Annotations by Codon page for more information about this feature. Methods For a description of the Genscan program and the model that underlies it, refer to Burge and Karlin (1997) in the References section below. The splice site models used are described in more detail in Burge (1998) below. Credits Thanks to Chris Burge for providing the Genscan program. References Burge C. Modeling Dependencies in Pre-mRNA Splicing Signals. In: Salzberg S, Searls D, Kasif S, editors. Computational Methods in Molecular Biology. Amsterdam: Elsevier Science; 1998. p. 127-163. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 1997 Apr 25;268(1):78-94.