Schema for CDS Mapping - TBLASTN Mapping of D. melanogaster CDS

Database: DbusGB1 Primary Table: cds_mapping Row Count: 60,847 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	CP012523	`varchar(255)`	values
`chromStart`	94410	`int(10) unsigned`	range
`chromEnd`	94605	`int(10) unsigned`	range
`name`	CG34408:1_11831_0	`varchar(255)`	values
`score`	814	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	94410	`int(10) unsigned`	range
`thickEnd`	94605	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(11)`	range
`blockSizes`	156,36,	`longblob`
`chromStarts`	0,159,	`longblob`
`id`	CG34408:1_11831_0	`varchar(255)`	values
`description`	E-value: 1.9...	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
CP012523	94410	94605	CG34408:1_11831_0	814	+	94410	94605	2	156,36,	0,159,	CG34408:1_11831_0	E-value: 1.9e-37Reading frame: +1Bit score: 151Percent identity: ...
CP012523	94667	94886	CG34408:2_11831_0	946	+	94667	94886	1	219,	0,	CG34408:2_11831_0	E-value: 2.0e-54Reading frame: +3Bit score: 207Percent identity: ...
CP012523	95083	95476	CG34408:4_11831_2	864	+	95083	95476	1	393,	0,	CG34408:4_11831_2	E-value: 7.9e-95Reading frame: +2Bit score: 341Percent identity: ...
CP012523	95542	95800	CG34408:5_11831_2	838	+	95542	95800	1	258,	0,	CG34408:5_11831_2	E-value: 6.8e-60Reading frame: +2Bit score: 225Percent identity: ...
CP012523	95960	96386	CG34408:6_11831_2	426	+	95960	96386	7	153,120,48,30,6,6,9,	0,198,318,366,399,408,417,	CG34408:6_11831_2	E-value: 1.2e-52Reading frame: +3Bit score: 201Percent identity: ...
CP012523	96158	96185	CG34408:15_11831_0	500	+	96158	96185	2	21,3,	0,24,	CG34408:15_11831_0	E-value: 2.5e-142Reading frame: +3Bit score: 21Percent identity: ...
CP012523	96269	96494	CG34408:7_11831_0	428	+	96269	96494	7	36,6,15,63,6,12,75,	0,36,42,57,120,126,150,	CG34408:7_11831_0	E-value: 2.1e-24Reading frame: +3Bit score: 107Percent identity: ...
CP012523	96979	97117	CG34408:9_11831_2	732	+	96979	97117	4	6,12,6,102,	0,6,18,36,	CG34408:9_11831_2	E-value: 2.9e-18Reading frame: +2Bit score: 87Percent identity: 7 ...
CP012523	97183	97705	CG34408:10_11831_2	874	+	97183	97705	1	522,	0,	CG34408:10_11831_2	E-value: 3.5e-125Reading frame: +2Bit score: 442Percent identity: ...
CP012523	97791	97995	CG34408:11_11831_1	524	+	97791	97995	6	150,9,3,9,9,21,	0,150,159,162,171,183,	CG34408:11_11831_1	E-value: 1.9e-33Reading frame: +1Bit score: 137Percent identity: ...

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

CDS Mapping (cds_mapping) Track Description


	Description This track shows the tblastn alignment of the coding exons of D. melanogaster genes against the D. busckii genome. The coding exon sequences were obtained from FlyBase. The tblastn search was performed using the following parameters: `-e=1e-2 -topComboN=1 -links -hspsepSmax=10000 -hspsepQmax=1000 -matrix=PAM40 -Q=7 -R=2` References St Pierre SE, Ponting L, Stefancsik R, McQuilton P; FlyBase Consortium. FlyBase 102 — advanced approaches to interrogating FlyBase. Nucleic Acids Res. 2014 Jan;42(Database issue):D780-8 Gish, W. WU BLAST 2.0. (1996-2006)

Description

References