Schema for N-SCAN - N-SCAN Gene Predictions

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Schema for N-SCAN - N-SCAN Gene Predictions

Database: DkikGB2 Primary Table: nscan Row Count: 13,420

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	AFFH02000026.001.1	`varchar(255)`	values
`chrom`	AFFH02000026	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	669	`int(10) unsigned`	range
`txEnd`	1644	`int(10) unsigned`	range
`cdsStart`	669	`int(10) unsigned`	range
`cdsEnd`	1644	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	669,1030,	`longblob`
`exonEnds`	971,1644,	`longblob`
`score`	0	`int(11)`	range
`name2`	AFFH02000026.001	`varchar(255)`	values
`cdsStartStat`	cmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	incmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,2,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	AFFH02000026.001.1	AFFH02000026	-	669	1644	669	1644	2	669,1030,	971,1644,	0	AFFH02000026.001	cmpl	incmpl	1,2,
585	AFFH02000049.001.1	AFFH02000049	+	2313	2602	2313	2602	1	2313,	2602,	0	AFFH02000049.001	incmpl	incmpl	0,
585	AFFH02000236.001.1	AFFH02000236	-	51	405	51	405	1	51,	405,	0	AFFH02000236.001	cmpl	incmpl	0,
585	AFFH02000335.001.1	AFFH02000335	+	48277	58251	48371	58251	7	48277,48679,49060,49668,53028,56634,58115,	48386,48997,49609,49853,55630,56729,58251,	0	AFFH02000335.001	cmpl	cmpl	0,0,0,0,2,0,2,
585	AFFH02000335.002.1	AFFH02000335	+	59834	62179	60056	62179	4	59834,60700,60943,61628,	60640,60855,61570,62179,	0	AFFH02000335.002	cmpl	cmpl	0,2,1,1,
585	AFFH02000335.003.1	AFFH02000335	+	63167	67887	64891	67887	5	63167,64860,65637,67284,67489,	63481,65570,66144,67428,67887,	0	AFFH02000335.003	cmpl	cmpl	-1,0,1,1,1,
585	AFFH02000335.004.1	AFFH02000335	-	68143	70069	68143	70056	8	68143,68306,68573,68906,69421,69575,69703,69983,	68210,68517,68851,69361,69517,69643,69928,70069,	0	AFFH02000335.004	cmpl	cmpl	2,1,2,0,0,1,1,0,
585	AFFH02000335.005.1	AFFH02000335	+	70580	72729	70931	72729	2	70580,71728,	71670,72729,	0	AFFH02000335.005	cmpl	cmpl	0,1,
585	AFFH02000335.006.1	AFFH02000335	+	73747	74684	73844	74684	3	73747,74134,74354,	74070,74226,74684,	0	AFFH02000335.006	cmpl	cmpl	0,1,0,
585	AFFH02000335.007.1	AFFH02000335	-	76364	84583	76364	84326	5	76364,77736,80840,83724,84276,	77143,78703,81016,83999,84583,	0	AFFH02000335.007	cmpl	cmpl	1,0,1,2,0,

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.