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

Database: DkikGB2 Primary Table: spalnDm3Proteins Row Count: 28,096 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFH02000335	`varchar(255)`	values
`chromStart`	35163	`int(10) unsigned`	range
`chromEnd`	35457	`int(10) unsigned`	range
`name`	CG4783-PA	`varchar(255)`	values
`score`	340	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	35163	`int(10) unsigned`	range
`thickEnd`	35457	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	178,59,	`longblob`
`chromStarts`	0,235	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFH02000335	35163	35457	CG4783-PA	340	-	35163	35457	2	178,59,	0,235
585	AFFH02000335	35163	35457	CG4783-PB	351	-	35163	35457	2	178,59,	0,235
585	AFFH02000335	36142	58248	Hs6st-PA	2152	+	36142	58248	6	76,113,318,549,185,133,	0,437,12537,12918,13526,21973
585	AFFH02000335	36142	58248	Hs6st-PB	2152	+	36142	58248	6	76,113,318,549,185,133,	0,437,12537,12918,13526,21973
585	AFFH02000335	53149	55651	mira-PA	4179	+	53149	55651	1	2502,	0
585	AFFH02000335	53149	55651	mira-PB	4020	+	53149	55651	2	1785,627,	0,1875
585	AFFH02000335	53149	55651	mira-PC	4046	+	53149	55651	2	1785,645,	0,1857
585	AFFH02000335	60056	62176	CG4459-PA	3191	+	60056	62176	4	584,155,627,548,	0,644,887,1572
585	AFFH02000335	64891	67884	CG4462-PA	3076	+	64891	67884	4	679,507,144,395,	0,746,2393,2598
585	AFFH02000335	68146	70056	CG4770-PA	2608	-	68146	70056	8	64,211,278,455,96,68,225,73,	0,160,427,760,1275,1429,1557,1837

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. kikkawai genome assembly using Spaln2 with cross-species parameters.

Methods

D. melanogaster proteins were mapped against the D. kikkawai 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