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

Database: DpseGB3 Primary Table: cds_mapping Row Count: 62,339 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	CH379058	`varchar(255)`	values
`chromStart`	17126	`int(10) unsigned`	range
`chromEnd`	19907	`int(10) unsigned`	range
`name`	CG13991:1_4192_0	`varchar(255)`	values
`score`	598	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	17126	`int(10) unsigned`	range
`thickEnd`	19907	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	12	`int(11)`	range
`blockSizes`	282,54,12,777,18,3,6,18,3,6...	`longblob`
`chromStarts`	0,285,339,357,1143,1164,116...	`longblob`
`id`	CG13991:1_4192_0	`varchar(255)`	values
`description`	E-value: 0.<...	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
CH379058	17126	19907	CG13991:1_4192_0	598	-	17126	19907	12	282,54,12,777,18,3,6,18,3,6,1554,6,	0,285,339,357,1143,1164,1167,1182,1200,1206,1218,2775,	CG13991:1_4192_0	E-value: 0.Reading frame: -3Bit score: 1944Percent identity: 77.9 ...
CH379058	20234	22544	CG13991:1_4192_0	488	-	20234	22544	28	9,24,9,54,9,3,3,21,51,3,72,825,3,6,6,135,9,591,21,9,18,198,75,6,9,21,9,9,	0,9,48,63,120,138,141,144,171,225,228,306,1134,1140,1146,1155,1290,1302,1914,1935,1944,1965,2163,2253,2262,2271,2292,2301,	CG13991:1_4192_0	E-value: 0.Reading frame: -3Bit score: 1311Percent identity: 69.3 ...
CH379058	27003	27153	CG33632:3_11275_0	494	-	27003	27153	4	30,3,6,99,	0,30,45,51,	CG33632:3_11275_0	E-value: 2.0e-18Reading frame: -2Bit score: 88Percent identity: 6 ...
CH379058	27003	27153	dls:3_11301_0	270	-	27003	27153	7	24,6,9,3,6,60,15,	0,24,30,60,66,75,135,	dls:3_11301_0	E-value: 2.8e-08Reading frame: -2Bit score: 54Percent identity: 4 ...
CH379058	27003	27156	CG33689:3_11300_0	192	-	27003	27156	13	24,6,3,3,6,18,6,24,3,21,3,3,6,	0,24,30,39,45,54,72,84,114,117,138,141,147,	CG33689:3_11300_0	E-value: 6.1e-08Reading frame: -2Bit score: 53Percent identity: 4 ...
CH379058	27003	27159	CG33922:3_11442_0	454	-	27003	27159	5	30,3,33,15,69,	0,30,36,72,87,	CG33922:3_11442_0	E-value: 1.2e-19Reading frame: -2Bit score: 92Percent identity: 6 ...
CH379058	27003	27168	CG33777:3_11325_0	308	-	27003	27168	4	30,3,6,114,	0,30,45,51,	CG33777:3_11325_0	E-value: 9.6e-14Reading frame: -2Bit score: 72Percent identity: 5 ...
CH379058	27003	27168	CG33798:3_11331_0	360	-	27003	27168	5	24,3,3,3,123,	0,24,30,39,42,	CG33798:3_11331_0	E-value: 1.2e-18Reading frame: -2Bit score: 88Percent identity: 6 ...
CH379058	27257	27368	CG33648:3_11285_0	472	-	27257	27368	8	12,30,3,3,3,3,3,30,	0,18,48,54,60,63,72,81,	CG33648:3_11285_0	E-value: 0.00018Reading frame: -3Bit score: 41Percent identity: 5 ...
CH379058	42267	42300	CG33700:1_11303_0	152	-	42267	42300	3	12,12,9,	0,12,24,	CG33700:1_11303_0	E-value: 3.8e-05Reading frame: -2Bit score: 22Percent identity: 6 ...

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. pseudoobscura 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