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

Database: DmirGB2 Primary Table: spalnDm3Proteins Row Count: 26,934 Data last updated: 2024-01-05

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CM001516	`varchar(255)`	values
`chromStart`	15164	`int(10) unsigned`	range
`chromEnd`	16787	`int(10) unsigned`	range
`name`	Cyp311a1-PB	`varchar(255)`	values
`score`	1922	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	15164	`int(10) unsigned`	range
`thickEnd`	16787	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	4	`int(10) unsigned`	range
`blockSizes`	151,378,348,569,	`longblob`
`chromStarts`	0,217,646,1054	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	CM001516	15164	16787	Cyp311a1-PB	1922	+	15164	16787	4	151,378,348,569,	0,217,646,1054
585	CM001516	16973	17984	CG14106-PA	707	+	16973	17984	1	1011,	0
585	CM001516	18571	21010	CG4281-PA	2194	+	18571	21010	4	118,303,1607,193,	0,176,559,2246
585	CM001516	23489	29357	Sik2-PA	4998	+	23489	29357	9	624,64,287,480,630,327,89,1735,105,	0,690,820,1209,1782,2480,2861,3023,5763
585	CM001516	30533	31729	CG4313-PC	1420	-	30533	31729	2	484,635,	0,561
585	CM001516	30533	31729	CG4313-PE	1420	-	30533	31729	2	484,635,	0,561
585	CM001516	30533	44064	CG4313-PD	2088	-	30533	44064	4	484,663,471,71,	0,561,1293,13460
585	CM001516	41785	44238	moody-PC	2466	+	41785	44238	4	101,141,1001,659,	0,489,719,1794
585	CM001516	41785	44238	moody-PD	2466	+	41785	44238	4	101,141,1001,659,	0,489,719,1794
585	CM001516	41785	44347	moody-PA	2661	+	41785	44347	4	101,141,1001,770,	0,489,719,1792

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

Methods

D. melanogaster proteins were mapped against the D. miranda 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