Schema for N-SCAN - N-SCAN Gene Predictions

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Schema for N-SCAN - N-SCAN Gene Predictions

Database: DtakGB2 Primary Table: nscan Row Count: 13,885

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	AFFI02000003.001.1	`varchar(255)`	values
`chrom`	AFFI02000003	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	10545	`int(10) unsigned`	range
`txEnd`	32483	`int(10) unsigned`	range
`cdsStart`	10545	`int(10) unsigned`	range
`cdsEnd`	32417	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	10545,30912,31975,	`longblob`
`exonEnds`	11330,31179,32483,	`longblob`
`score`	0	`int(11)`	range
`name2`	AFFI02000003.001	`varchar(255)`	values
`cdsStartStat`	cmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	cmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	AFFI02000003.001.1	AFFI02000003	-	10545	32483	10545	32417	3	10545,30912,31975,	11330,31179,32483,	0	AFFI02000003.001	cmpl	cmpl	1,1,0,
585	AFFI02000003.002.1	AFFI02000003	+	39068	42477	39375	42477	3	39068,39349,39950,	39141,39896,42477,	0	AFFI02000003.002	cmpl	cmpl	-1,0,2,
585	AFFI02000009.001.1	AFFI02000009	+	9178	17120	10234	17120	5	9178,10222,11516,15454,16065,	9275,11046,12293,15708,17120,	0	AFFI02000009.001	cmpl	cmpl	-1,0,2,2,1,
585	AFFI02000009.002.1	AFFI02000009	+	17584	19534	17689	19534	3	17584,18383,19046,	18043,18780,19534,	0	AFFI02000009.002	cmpl	cmpl	0,0,1,
585	AFFI02000009.003.1	AFFI02000009	+	19826	20195	19833	20195	2	19826,20060,	19983,20195,	0	AFFI02000009.003	cmpl	cmpl	0,0,
585	AFFI02000009.004.1	AFFI02000009	+	20915	25481	21249	25481	4	20915,24069,24284,25295,	21321,24204,24644,25481,	0	AFFI02000009.004	cmpl	cmpl	0,0,0,0,
585	AFFI02000009.005.1	AFFI02000009	-	26034	26373	26034	26334	1	26034,	26373,	0	AFFI02000009.005	cmpl	cmpl	0,
585	AFFI02000009.006.1	AFFI02000009	+	27082	27467	27122	27467	1	27082,	27467,	0	AFFI02000009.006	cmpl	cmpl	0,
585	AFFI02000021.001.1	AFFI02000021	-	5215	8397	5215	8363	5	5215,6380,6947,7456,8152,	6318,6533,7367,7795,8397,	0	AFFI02000021.001	cmpl	cmpl	1,1,1,1,0,
585	AFFI02000021.002.1	AFFI02000021	+	9846	11211	10218	11211	1	9846,	11211,	0	AFFI02000021.002	cmpl	cmpl	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.