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

Database: DgriCAF1 Primary Table: spalnDm3Proteins Row Count: 26,078 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_10030	`varchar(255)`	values
`chromStart`	5624	`int(10) unsigned`	range
`chromEnd`	22525	`int(10) unsigned`	range
`name`	SMC5-PE	`varchar(255)`	values
`score`	2985	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	5624	`int(10) unsigned`	range
`thickEnd`	22525	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	17	`int(10) unsigned`	range
`blockSizes`	74,373,179,247,99,288,102,2...	`longblob`
`chromStarts`	0,1126,1584,2755,3072,3227,...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	scaffold_10030	5624	22525	SMC5-PE	2985	+	5624	22525	17	74,373,179,247,99,288,102,209,164,127,206,218,225,225,158,118,93,	0,1126,1584,2755,3072,3227,3586,9515,9781,10130,10945,11209,11483,11770,16131,16631,16808
585	scaffold_10030	5624	22525	SMC5-PF	2933	+	5624	22525	16	74,373,179,247,288,102,209,164,127,206,218,225,225,158,118,93,	0,1126,1584,2755,3227,3586,9515,9781,10130,10945,11209,11483,11770,16131,16631,16808
585	scaffold_10030	5624	22525	SMC5-PG	2920	+	5624	22525	17	74,373,179,247,99,288,102,209,164,127,206,218,225,225,158,118,93,	0,1126,1584,2755,3072,3227,3586,9515,9781,10130,10945,11209,11483,11770,16131,16631,16808
585	scaffold_10030	5624	22525	SMC5-PH	2868	+	5624	22525	16	74,373,179,247,288,102,209,164,127,206,218,225,225,158,118,93,	0,1126,1584,2755,3227,3586,9515,9781,10130,10945,11209,11483,11770,16131,16631,16808
585	scaffold_10033	315	881	CG30270-PE	354	+	315	881	2	48,456,	0,110
585	scaffold_10033	444	881	CG30270-PF	330	+	444	881	2	35,340,	0,97
585	scaffold_10068	0	1348	ORY-PD	558	-	0	1348	2	220,249,	0,1099
585	scaffold_10090	10	586	CG33263-PA	625	-	10	586	1	576,	0
585	scaffold_10869	224	563	CG15152-PA	510	-	224	563	1	339,	0
585	scaffold_10869	224	563	CG15152-PB	510	-	224	563	1	339,	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. grimshawi genome assembly using Spaln2 with cross-species parameters.

Methods

D. melanogaster proteins were mapped against the D. grimshawi 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