Schema for D. mel Proteins - Spaln Alignment of D. melanogaster Proteins

Database: DnavGB1 Primary Table: spalnDm3Proteins Row Count: 23,292 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	LSRL01000001	`varchar(255)`	values
`chromStart`	63531	`int(10) unsigned`	range
`chromEnd`	67164	`int(10) unsigned`	range
`name`	Coq8-PA	`varchar(255)`	values
`score`	2958	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	63531	`int(10) unsigned`	range
`thickEnd`	67164	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	3	`int(10) unsigned`	range
`blockSizes`	550,820,712,	`longblob`
`chromStarts`	0,1477,2921	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	LSRL01000001	63531	67164	Coq8-PA	2958	-	63531	67164	3	550,820,712,	0,1477,2921
585	LSRL01000001	67993	69784	CG17486-PB	1854	+	67993	69784	2	371,1360,	0,431
585	LSRL01000001	71877	72832	Flad1-PB	982	-	71877	72832	2	294,603,	0,352
585	LSRL01000001	71877	94491	Flad1-PA	972	-	71877	94491	3	294,582,51,	0,352,22563
585	LSRL01000001	73846	76684	CG4404-PA	954	-	73846	76684	4	218,382,170,154,	0,284,903,2684
585	LSRL01000001	79409	80323	Brms1-PA	1258	-	79409	80323	3	339,245,193,	0,410,721
585	LSRL01000001	80959	82271	CG4645-PA	1506	+	80959	82271	4	501,207,93,294,	0,572,866,1018
585	LSRL01000001	80959	82271	CG4645-PB	1506	+	80959	82271	4	501,207,93,294,	0,572,866,1018
585	LSRL01000001	80959	82271	CG4645-PC	1506	+	80959	82271	4	501,207,93,294,	0,572,866,1018
585	LSRL01000001	81166	108482	Rbp9-PB	1274	+	81166	108482	7	120,107,72,155,258,289,322,	0,465,18111,23294,23900,24247,26994

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

D. mel Proteins (spalnDm3Proteins) Track Description

Description

D. melanogaster proteins annotated by FlyBase were aligned against the D. navojoa genome assembly using Spaln2 with cross-species parameters.

Methods

D. melanogaster proteins were mapped against the D. navojoa genome assembly with tblastn. For each protein, the region surrounding the best tblastn hit is identified and each protein is re-aligned against this genomic region with Spaln2 using cross-species parameters optimized for D. melanogaster: (-Tdromel -yX).

References

Iwata H., and Gotoh, O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Research. 2012, 109