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

Database: DereCAF1 Primary Table: cds_mapping Row Count: 63,399 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	scaffold_1026	`varchar(255)`	values
`chromStart`	1137	`int(10) unsigned`	range
`chromEnd`	1263	`int(10) unsigned`	range
`name`	His3.3B:2_850_0	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	1137	`int(10) unsigned`	range
`thickEnd`	1263	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	126,	`longblob`
`chromStarts`	0,	`longblob`
`id`	His3.3B:2_850_0	`varchar(255)`	values
`description`	E-value: 1.5...	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
scaffold_1026	1137	1263	His3.3B:2_850_0	1000	-	1137	1263	1	126,	0,	His3.3B:2_850_0	E-value: 1.5e-27Reading frame: -3Bit score: 117Percent identity: ...
scaffold_1026	1137	1263	His3.3A:2_1404_0	1000	-	1137	1263	1	126,	0,	His3.3A:2_1404_0	E-value: 1.5e-27Reading frame: -3Bit score: 117Percent identity: ...
scaffold_1030	69	834	His1:CG31617:1_10557_0	768	-	69	834	2	666,99,	0,666,	His1:CG31617:1_10557_0	E-value: 1.4e-155Reading frame: -2Bit score: 538Percent identity: ...
scaffold_1030	69	834	His1:CG33801:1_11332_0	760	-	69	834	2	666,99,	0,666,	His1:CG33801:1_11332_0	E-value: 1.4e-154Reading frame: -2Bit score: 535Percent identity: ...
scaffold_1030	69	834	His1:CG33804:1_11334_0	768	-	69	834	2	666,99,	0,666,	His1:CG33804:1_11334_0	E-value: 1.4e-155Reading frame: -2Bit score: 538Percent identity: ...
scaffold_1030	69	834	His1:CG33807:1_11336_0	760	-	69	834	2	666,99,	0,666,	His1:CG33807:1_11336_0	E-value: 1.8e-154Reading frame: -2Bit score: 535Percent identity: ...
scaffold_1030	69	834	His1:CG33810:1_11339_0	768	-	69	834	2	666,99,	0,666,	His1:CG33810:1_11339_0	E-value: 1.4e-155Reading frame: -2Bit score: 538Percent identity: ...
scaffold_1030	69	834	His1:CG33813:1_11341_0	768	-	69	834	2	666,99,	0,666,	His1:CG33813:1_11341_0	E-value: 1.4e-155Reading frame: -2Bit score: 538Percent identity: ...
scaffold_1030	69	834	His1:CG33816:1_11344_0	768	-	69	834	2	666,99,	0,666,	His1:CG33816:1_11344_0	E-value: 1.4e-155Reading frame: -2Bit score: 538Percent identity: ...
scaffold_1030	69	834	His1:CG33819:1_11347_0	768	-	69	834	2	666,99,	0,666,	His1:CG33819:1_11347_0	E-value: 1.4e-155Reading frame: -2Bit score: 538Percent 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. erecta 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