Schema for N-SCAN - N-SCAN Gene Predictions

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Schema for N-SCAN - N-SCAN Gene Predictions

Database: DsuzGB1 Primary Table: nscan Row Count: 14,779

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	AWUT01012676.001.1	`varchar(255)`	values
`chrom`	AWUT01012676	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	21759	`int(10) unsigned`	range
`txEnd`	65395	`int(10) unsigned`	range
`cdsStart`	21759	`int(10) unsigned`	range
`cdsEnd`	44753	`int(10) unsigned`	range
`exonCount`	4	`int(10) unsigned`	range
`exonStarts`	21759,22150,44639,65024,	`longblob`
`exonEnds`	22097,22292,44809,65395,	`longblob`
`score`	0	`int(11)`	range
`name2`	AWUT01012676.001	`varchar(255)`	values
`cdsStartStat`	cmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	cmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,0,0,-1,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	AWUT01012676.001.1	AWUT01012676	-	21759	65395	21759	44753	4	21759,22150,44639,65024,	22097,22292,44809,65395,	0	AWUT01012676.001	cmpl	cmpl	1,0,0,-1,
585	AWUT01013449.001.1	AWUT01013449	+	8266	63318	8278	63318	8	8266,8440,56665,57355,57606,57866,58731,63272,	8365,9051,57299,57548,57815,58676,58889,63318,	0	AWUT01013449.001	cmpl	cmpl	0,0,2,0,1,0,0,2,
585	AWUT01013449.002.1	AWUT01013449	-	68398	68854	68398	68854	1	68398,	68854,	0	AWUT01013449.002	cmpl	incmpl	0,
585	AWUT01014658.001.1	AWUT01014658	+	28226	39390	28226	39390	2	28226,39277,	28394,39390,	0	AWUT01014658.001	incmpl	incmpl	0,0,
585	AWUT01014734.001.1	AWUT01014734	+	16193	19765	16305	19765	6	16193,16352,17219,17480,17725,18686,	16308,16460,17454,17659,17885,19765,	0	AWUT01014734.001	cmpl	cmpl	0,0,0,1,0,1,
585	AWUT01014734.002.1	AWUT01014734	-	25556	30323	25556	30300	2	25556,29783,	27736,30323,	0	AWUT01014734.002	cmpl	cmpl	1,0,
585	AWUT01015089.001.1	AWUT01015089	+	3075	22675	3075	22675	5	3075,3487,3812,19472,22477,	3433,3762,3994,19589,22675,	0	AWUT01015089.001	incmpl	incmpl	1,2,1,0,0,
585	AWUT01015096.001.1	AWUT01015096	-	13784	14019	13784	14019	1	13784,	14019,	0	AWUT01015096.001	incmpl	incmpl	1,
585	AWUT01015145.001.1	AWUT01015145	+	26546	28319	26555	28319	2	26546,27299,	27197,28319,	0	AWUT01015145.001	cmpl	cmpl	0,0,
585	AWUT01015241.001.1	AWUT01015241	-	4905	7036	4905	6989	2	4905,6860,	5169,7036,	0	AWUT01015241.001	cmpl	cmpl	0,0,

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.