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

Database: DmojCAF1 Primary Table: spalnDm3Proteins Row Count: 26,268 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_1740	`varchar(255)`	values
`chromStart`	1860	`int(10) unsigned`	range
`chromEnd`	3428	`int(10) unsigned`	range
`name`	Cyp6a9-PB	`varchar(255)`	values
`score`	2269	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	1860	`int(10) unsigned`	range
`thickEnd`	3428	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	416,1096,	`longblob`
`chromStarts`	0,472	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	scaffold_1740	1860	3428	Cyp6a9-PB	2269	-	1860	3428	2	416,1096,	0,472
585	scaffold_1745	91	3415	CG32032-PA	754	-	91	3415	4	438,111,122,31,	0,492,3036,3293
585	scaffold_1786	25	3527	Ubi-p5E-PA	2852	+	25	3527	2	1594,8,	0,3494
585	scaffold_1786	25	3527	Ubi-p5E-PB	2852	+	25	3527	2	1594,8,	0,3494
585	scaffold_1786	937	1825	CG11700-PB	1527	+	937	1825	1	888,	0
585	scaffold_1786	3934	4511	Lamtor4-PB	617	-	3934	4511	2	370,146,	0,431
585	scaffold_1786	4090	4511	Lamtor4-PA	541	-	4090	4511	2	214,146,	0,275
585	scaffold_1920	2100	3671	sals-PA	2306	+	2100	3671	1	1571,	0
585	scaffold_2860	8878	9896	ORY-PD	1432	-	8878	9896	2	322,623,	0,395
585	scaffold_3108	336	744	His3:CG33824-PA	776	+	336	744	1	408,	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. mojavensis genome assembly using Spaln2 with cross-species parameters.

Methods

D. melanogaster proteins were mapped against the D. mojavensis 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