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

Database: DyakCAF1 Primary Table: spalnDm3Proteins Row Count: 30,088 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	8646	`int(10) unsigned`	range
`chromEnd`	12822	`int(10) unsigned`	range
`name`	l(2)gl-PE	`varchar(255)`	values
`score`	5452	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	8646	`int(10) unsigned`	range
`thickEnd`	12822	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	7	`int(10) unsigned`	range
`blockSizes`	127,109,443,643,106,1192,716,	`longblob`
`chromStarts`	0,190,633,1138,2047,2210,3460	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	chr2L	8646	12822	l(2)gl-PE	5452	-	8646	12822	7	127,109,443,643,106,1192,716,	0,190,633,1138,2047,2210,3460
585	chr2L	8646	12822	l(2)gl-PD	5452	-	8646	12822	7	127,109,443,643,106,1192,716,	0,190,633,1138,2047,2210,3460
585	chr2L	8646	12822	l(2)gl-PF	5452	-	8646	12822	7	127,109,443,643,106,1192,716,	0,190,633,1138,2047,2210,3460
585	chr2L	8646	14684	l(2)gl-PA	5698	-	8646	14684	8	127,109,443,643,106,1192,779,84,	0,190,633,1138,2047,2210,3460,5954
585	chr2L	8646	14684	l(2)gl-PB	5617	-	8646	14684	8	127,109,443,643,106,1192,779,84,	0,190,633,1138,2047,2210,3460,5954
585	chr2L	8646	14684	l(2)gl-PC	5698	-	8646	14684	8	127,109,443,643,106,1192,779,84,	0,190,633,1138,2047,2210,3460,5954
585	chr2L	8646	14684	l(2)gl-PG	5698	-	8646	14684	8	127,109,443,643,106,1192,779,84,	0,190,633,1138,2047,2210,3460,5954
585	chr2L	8646	14684	l(2)gl-PH	5698	-	8646	14684	8	127,109,443,643,106,1192,779,84,	0,190,633,1138,2047,2210,3460,5954
585	chr2L	8646	14684	l(2)gl-PI	5698	-	8646	14684	8	127,109,443,643,106,1192,779,84,	0,190,633,1138,2047,2210,3460,5954
585	chr2L	8646	14684	l(2)gl-PJ	5698	-	8646	14684	8	127,109,443,643,106,1192,779,84,	0,190,633,1138,2047,2210,3460,5954

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

Methods

D. melanogaster proteins were mapped against the D. yakuba 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