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

Database: DanaCAF1 Primary Table: spalnDm3Proteins Row Count: 28,001 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_10492	`varchar(255)`	values
`chromStart`	59	`int(10) unsigned`	range
`chromEnd`	515	`int(10) unsigned`	range
`name`	CG5004-PF	`varchar(255)`	values
`score`	548	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	59	`int(10) unsigned`	range
`thickEnd`	515	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	132,174,	`longblob`
`chromStarts`	0,282	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	scaffold_10492	59	515	CG5004-PF	548	+	59	515	2	132,174,	0,282
585	scaffold_10492	59	515	CG5004-PD	548	+	59	515	2	132,174,	0,282
585	scaffold_10492	59	515	CG5004-PE	548	+	59	515	2	132,174,	0,282
586	scaffold_10513	142336	147674	Rad23-PB	1056	-	142336	147674	4	108,297,95,502,	0,199,552,4836
586	scaffold_10513	142336	167315	Rad23-PA	1356	-	142336	167315	5	108,297,95,649,66,	0,199,552,4836,24913
586	scaffold_10513	142336	167315	Rad23-PC	1356	-	142336	167315	5	108,297,95,649,66,	0,199,552,4836,24913
585	scaffold_12413	10380	10869	CG5104-PB	830	+	10380	10869	1	489,	0
585	scaffold_12422	80059	87160	Ir40a-PE	1003	+	80059	87160	4	4,505,263,134,	0,6090,6650,6967
585	scaffold_12422	84372	87160	Ir40a-PF	2533	+	84372	87160	7	103,569,255,412,505,263,134,	0,158,779,1090,1777,2337,2654
585	scaffold_12422	86316	87160	Ir40a-PG	753	+	86316	87160	3	338,263,134,	0,393,710

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

Methods

D. melanogaster proteins were mapped against the D. ananassae 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