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

Database: DvirCAF1 Primary Table: spalnDm3Proteins Row Count: 26,432 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_10318	`varchar(255)`	values
`chromStart`	4351	`int(10) unsigned`	range
`chromEnd`	5023	`int(10) unsigned`	range
`name`	mt:ATPase6-PB	`varchar(255)`	values
`score`	777	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	4351	`int(10) unsigned`	range
`thickEnd`	5023	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	672,	`longblob`
`chromStarts`	0	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	scaffold_10318	4351	5023	mt:ATPase6-PB	777	+	4351	5023	1	672,	0
585	scaffold_10322	8724	55181	Eip63F-1-PA	768	+	8724	55181	5	115,144,154,149,20,	0,38275,44518,44728,46437
585	scaffold_10322	30728	55181	Eip63F-1-PC	782	+	30728	55181	5	91,144,154,149,20,	0,16271,22514,22724,24433
585	scaffold_10322	43041	55181	Eip63F-1-PD	847	+	43041	55181	5	34,144,154,149,20,	0,3958,10201,10411,12120
585	scaffold_10322	46256	55181	Eip63F-1-PB	789	+	46256	55181	5	19,144,154,149,20,	0,743,6986,7196,8905
585	scaffold_10322	57602	58665	mge-PB	555	+	57602	58665	3	21,42,306,	0,622,757
585	scaffold_10322	57956	58290	mge-PC	261	+	57956	58290	2	102,66,	0,268
585	scaffold_10322	57956	58665	mge-PA	702	+	57956	58665	3	102,42,306,	0,268,403
585	scaffold_10322	59212	62374	ida-PA	3455	-	59212	62374	3	2118,122,79,	0,2185,3083
585	scaffold_10322	62230	63856	Sc2-PA	1532	-	62230	63856	5	202,116,217,228,146,	0,261,440,1184,1480

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

Methods

D. melanogaster proteins were mapped against the D. virilis 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