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

Database: DereCAF1 Primary Table: spalnDm3Proteins Row Count: 30,019 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_1390	`varchar(255)`	values
`chromStart`	1230	`int(10) unsigned`	range
`chromEnd`	3836	`int(10) unsigned`	range
`name`	mt:ND1-PB	`varchar(255)`	values
`score`	1199	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	1230	`int(10) unsigned`	range
`thickEnd`	3836	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	4,935,	`longblob`
`chromStarts`	0,1671	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	scaffold_1390	1230	3836	mt:ND1-PB	1199	+	1230	3836	2	4,935,	0,1671
585	scaffold_1390	3954	5067	mt:Cyt-b-PB	1409	-	3954	5067	1	1113,	0
585	scaffold_1390	5073	5985	mt:ND6-PA	697	-	5073	5985	2	530,4,	0,908
585	scaffold_1390	5730	6018	mt:ND4L-PA	439	+	5730	6018	1	288,	0
585	scaffold_1390	6020	7352	mt:ND4-PB	1378	+	6020	7352	1	1332,	0
585	scaffold_1390	7440	9123	mt:ND5-PB	1761	+	7440	9123	1	1683,	0
585	scaffold_1390	9649	11924	mt:ND3-PA	412	-	9649	11924	2	324,3,	0,2272
585	scaffold_1390	10074	10848	mt:CoIII-PA	710	-	10074	10848	1	774,	0
585	scaffold_1390	10850	11522	mt:ATPase6-PB	806	-	10850	11522	1	672,	0
585	scaffold_1390	11838	12501	mt:CoII-PA	850	-	11838	12501	1	663,	0

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

Methods

D. melanogaster proteins were mapped against the D. erecta 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