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

Database: DobsGB1 Primary Table: spalnDm3Proteins Row Count: 27,270 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	BDQP01000001	`varchar(255)`	values
`chromStart`	14012	`int(10) unsigned`	range
`chromEnd`	32201	`int(10) unsigned`	range
`name`	Ser-PA	`varchar(255)`	values
`score`	7004	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	14012	`int(10) unsigned`	range
`thickEnd`	32201	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	14	`int(10) unsigned`	range
`blockSizes`	312,118,188,55,316,134,176,...	`longblob`
`chromStarts`	0,4193,4958,9279,9659,11901...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	BDQP01000001	14012	32201	Ser-PA	7004	+	14012	32201	14	312,118,188,55,316,134,176,235,771,234,96,372,614,753,	0,4193,4958,9279,9659,11901,12173,12475,13900,14831,15137,16303,16761,17436
585	BDQP01000001	14012	32201	Ser-PB	7004	+	14012	32201	14	312,118,188,55,316,134,176,235,771,234,96,372,614,753,	0,4193,4958,9279,9659,11901,12173,12475,13900,14831,15137,16303,16761,17436
585	BDQP01000001	37924	40229	spn-D-PA	887	-	37924	40229	6	168,129,158,107,210,80,	0,262,454,670,845,2225
585	BDQP01000001	39761	41286	ppk31-PB	2108	-	39761	41286	5	164,107,656,217,152,	0,223,388,1103,1373
585	BDQP01000001	46006	47303	grass-PA	1774	-	46006	47303	5	422,194,49,214,126,	0,495,766,880,1171
585	BDQP01000001	46006	47487	grass-PB	1895	-	46006	47487	6	422,194,49,214,173,70,	0,495,766,880,1171,1411
585	BDQP01000001	48686	54552	Men-b-PC	3268	-	48686	54552	7	20,165,295,153,1050,190,17,	0,1047,1284,1649,1880,2993,5849
585	BDQP01000001	49660	54552	Men-b-PA	3255	-	49660	54552	7	32,129,295,153,1050,190,17,	0,109,310,675,906,2019,4875
585	BDQP01000001	49725	54552	Men-b-PB	3292	-	49725	54552	6	173,295,153,1050,190,17,	0,245,610,841,1954,4810
585	BDQP01000001	57234	76076	CG6051-PB	3969	+	57234	76076	5	36,141,741,968,1015,	0,15766,15980,16785,17827

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

Methods

D. melanogaster proteins were mapped against the D. obscura 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