Schema for N-SCAN Genes - N-SCAN Gene Predictions

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Schema for N-SCAN Genes - N-SCAN Gene Predictions

Database: dm3gene Primary Table: nscan Row Count: 2

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	chr3L.17.117.a	`varchar(255)`	values
`chrom`	contig1	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	5824	`int(10) unsigned`	range
`txEnd`	9497	`int(10) unsigned`	range
`cdsStart`	5934	`int(10) unsigned`	range
`cdsEnd`	9497	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	5824,6080,6898,	`longblob`
`exonEnds`	6019,6837,9497,	`longblob`
`score`	9373	`int(11)`	range
`name2`	chr3L.17.117	`varchar(255)`	values
`cdsStartStat`	cmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	cmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,1,2,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	chr3L.17.117.a	contig1	+	5824	9497	5934	9497	3	5824,6080,6898,	6019,6837,9497,	9373	chr3L.17.117	cmpl	cmpl	0,1,2,
585	chr3L.17.116.a	contig1	+	9725	10756	9863	10756	3	9725,10145,10606,	9897,10549,10756,	9372	chr3L.17.116	cmpl	cmpl	0,1,0,

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

N-SCAN Genes (nscan) Track Description


	Description This track shows gene predictions using the N-SCAN gene structure prediction program with multiple Drosophila species as informant. Methods N-SCAN combines biological-signal modeling in the target genome sequence along with information from a multiple-genome alignment to generate de novo gene predictions. It extends the TWINSCAN target-informant genome pair to allow for an arbitrary number of informant sequences as well as richer models of sequence evolution. N-SCAN models the phylogenetic relationships between the aligned genome sequences, context-dependent substitution rates, insertions, and deletions. References Gross SS, Brent MR. Using multiple alignments to improve gene prediction. In Proc. 9th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '05):374-388 and J Comput Biol. 2006 Mar;13(2):379-93. Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics. 2001 Jun 1;17(90001):S140-8.