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

Database: DtakGB2 Primary Table: spalnDm3Proteins Row Count: 29,368 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFI02000003	`varchar(255)`	values
`chromStart`	10548	`int(10) unsigned`	range
`chromEnd`	32417	`int(10) unsigned`	range
`name`	d4-PA	`varchar(255)`	values
`score`	2303	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	10548	`int(10) unsigned`	range
`thickEnd`	32417	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	3	`int(10) unsigned`	range
`blockSizes`	782,267,448,	`longblob`
`chromStarts`	0,20364,21421	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFI02000003	10548	32417	d4-PA	2303	-	10548	32417	3	782,267,448,	0,20364,21421
585	AFFI02000003	10548	31153	d4-PB	1560	-	10548	31153	2	782,241,	0,20364
585	AFFI02000003	10548	32417	d4-PC	2266	-	10548	32417	3	782,261,448,	0,20370,21421
585	AFFI02000003	10548	32417	d4-PD	2269	-	10548	32417	3	782,264,448,	0,20367,21421
585	AFFI02000003	39357	42474	CG3107-PA	4231	+	39357	42474	2	539,2524,	0,593
585	AFFI02000003	39357	42474	CG3107-PB	4231	+	39357	42474	2	539,2524,	0,593
585	AFFI02000003	39357	42474	CG3107-PC	4231	+	39357	42474	2	539,2524,	0,593
585	AFFI02000003	39357	42474	CG3107-PD	4231	+	39357	42474	2	539,2524,	0,593
585	AFFI02000009	10234	12294	yellow-e-PA	2831	+	10234	12294	2	812,778,	0,1282
585	AFFI02000009	15333	17117	yellow-e2-PB	2255	+	15333	17117	3	17,254,1052,	0,121,732

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

Methods

D. melanogaster proteins were mapped against the D. takahashii 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