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

Database: DsuzGB1 Primary Table: spalnDm3Proteins Row Count: 29,136 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AWUT01013449	`varchar(255)`	values
`chromStart`	8278	`int(10) unsigned`	range
`chromEnd`	60561	`int(10) unsigned`	range
`name`	IntS3-PA	`varchar(255)`	values
`score`	4841	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	8278	`int(10) unsigned`	range
`thickEnd`	60561	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	11	`int(10) unsigned`	range
`blockSizes`	87,611,634,193,209,810,158,...	`longblob`
`chromStarts`	0,162,48387,49077,49328,495...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AWUT01013449	8278	60561	IntS3-PA	4841	+	8278	60561	11	87,611,634,193,209,810,158,145,126,189,69,	0,162,48387,49077,49328,49588,50453,51590,51787,51971,52214
585	AWUT01014658	24770	39444	Fis1-PG	471	+	24770	39444	4	3,168,113,19,	0,3456,14507,14655
585	AWUT01014658	24770	39444	Fis1-PA	471	+	24770	39444	4	3,168,113,19,	0,3456,14507,14655
585	AWUT01014658	24770	39391	Fis1-PF	483	+	24770	39391	3	3,168,114,	0,3456,14507
585	AWUT01014658	24770	39391	Fis1-PD	483	+	24770	39391	3	3,168,114,	0,3456,14507
585	AWUT01014658	27877	39444	Fis1-PC	766	+	27877	39444	6	45,68,49,168,113,19,	0,102,243,349,11400,11548
585	AWUT01014658	27877	39391	Fis1-PE	778	+	27877	39391	5	45,68,49,168,114,	0,102,243,349,11400
585	AWUT01014734	2303	2384	CG46308-PA	181	+	2303	2384	1	81,	0
585	AWUT01014734	3206	19762	CG42784-PJ	2906	+	3206	19762	7	144,60,108,199,179,160,1076,	0,1827,13146,14013,14274,14519,15480
585	AWUT01014734	3206	19762	CG42784-PD	2823	+	3206	19762	6	144,108,199,179,160,1076,	0,13146,14013,14274,14519,15480

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

Spaln D. mel Proteins (spalnDm3Proteins) Track Description

Description

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

Methods

D. melanogaster proteins were mapped against the D. suzukii 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