Schema for N-SCAN - N-SCAN Gene Predictions

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Schema for N-SCAN - N-SCAN Gene Predictions

Database: DbiaGB2 Primary Table: nscan Row Count: 13,247

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	AFFD02000007.001.1	`varchar(255)`	values
`chrom`	AFFD02000007	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	1255	`int(10) unsigned`	range
`txEnd`	1885	`int(10) unsigned`	range
`cdsStart`	1255	`int(10) unsigned`	range
`cdsEnd`	1885	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	1255,1716,	`longblob`
`exonEnds`	1661,1885,	`longblob`
`score`	0	`int(11)`	range
`name2`	AFFD02000007.001	`varchar(255)`	values
`cdsStartStat`	incmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	incmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	AFFD02000007.001.1	AFFD02000007	-	1255	1885	1255	1885	2	1255,1716,	1661,1885,	0	AFFD02000007.001	incmpl	incmpl	1,0,
585	AFFD02000020.001.1	AFFD02000020	+	47	210	47	210	1	47,	210,	0	AFFD02000020.001	incmpl	incmpl	0,
585	AFFD02000032.001.1	AFFD02000032	+	57	137	57	137	1	57,	137,	0	AFFD02000032.001	incmpl	incmpl	0,
585	AFFD02000037.001.1	AFFD02000037	+	2886	3990	2935	3990	4	2886,3051,3441,3906,	2990,3188,3846,3990,	0	AFFD02000037.001	cmpl	cmpl	0,1,0,0,
585	AFFD02000037.002.1	AFFD02000037	+	5154	7468	5263	7468	4	5154,6079,6191,6627,	6022,6190,6244,7468,	0	AFFD02000037.002	cmpl	cmpl	0,0,0,2,
585	AFFD02000037.003.1	AFFD02000037	+	7688	15215	9164	15215	13	7688,9103,9460,10122,10784,11264,12565,12981,13492,13650,14015,14363,15008,	7965,9402,9668,10194,11106,12474,12925,13439,13591,13961,14298,14528,15215,	0	AFFD02000037.003	cmpl	cmpl	-1,0,1,2,2,0,1,1,0,0,2,0,0,
585	AFFD02000037.004.1	AFFD02000037	-	17690	21666	17690	21666	7	17690,18308,18793,19015,19326,19509,19767,	18257,18734,18958,19188,19449,19702,21666,	0	AFFD02000037.004	cmpl	incmpl	0,0,0,1,1,0,0,
585	AFFD02000052.001.1	AFFD02000052	-	652	975	652	975	1	652,	975,	0	AFFD02000052.001	incmpl	incmpl	0,
585	AFFD02000057.001.1	AFFD02000057	-	21	349	21	233	1	21,	349,	0	AFFD02000057.001	incmpl	cmpl	0,
585	AFFD02000073.001.1	AFFD02000073	+	3627	24552	3627	24552	2	3627,23538,	3733,24552,	0	AFFD02000073.001	incmpl	cmpl	2,0,

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

N-SCAN (nscan) Track Description


	Description This track shows the gene predictions produced by N-SCAN using D. melanogaster as the informant genome. References Gross SS, Brent MR. Using multiple alignments to improve gene prediction. J Comput Biol. 2006 Mar;13(2):379-93. doi: 10.1089/cmb.2006.13.379. Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics. 2001;17 Suppl 1:S140-8. doi: 10.1093/bioinformatics/17.suppl_1.s140.