Schema for D. mel Proteins - Spaln Alignment of D. melanogaster Proteins (FlyBase Release 5.53)

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Schema for D. mel Proteins - Spaln Alignment of D. melanogaster Proteins (FlyBase Release 5.53)

Database: DanaWGS Primary Table: spalnDm3Proteins Row Count: 26,366

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_10103	`varchar(255)`	values
`chromStart`	521	`int(10) unsigned`	range
`chromEnd`	3648	`int(10) unsigned`	range
`name`	CG16952-PC	`varchar(255)`	values
`score`	3543	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	521	`int(10) unsigned`	range
`thickEnd`	3648	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	3	`int(10) unsigned`	range
`blockSizes`	138,2476,402,	`longblob`
`chromStarts`	0,191,2725	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts
585	scaffold_10103	521	3648	CG16952-PC	3543	-	521	3648	0	3	138,2476,402,	0,191,2725
585	scaffold_10103	521	3648	CG16952-PB	3543	-	521	3648	0	3	138,2476,402,	0,191,2725
585	scaffold_10103	521	3648	CG16952-PD	3543	-	521	3648	0	3	138,2476,402,	0,191,2725
585	scaffold_10103	521	3648	CG16952-PE	3170	-	521	3648	0	2	2667,402,	0,2725
585	scaffold_10103	521	3648	CG16952-PA	3543	-	521	3648	0	3	138,2476,402,	0,191,2725
585	scaffold_10492	0	515	CG5004-PD	108	+	0	515	0	3	4,120,174,	0,71,341
585	scaffold_10492	0	515	CG5004-PE	108	+	0	515	0	3	4,120,174,	0,71,341
586	scaffold_10513	142336	147674	Rad23-PB	999	-	142336	147674	0	4	108,297,95,502,	0,199,552,4836
586	scaffold_10513	142336	167315	Rad23-PA	1295	-	142336	167315	0	5	108,297,95,649,66,	0,199,552,4836,24913
586	scaffold_10513	142336	167315	Rad23-PC	1295	-	142336	167315	0	5	108,297,95,649,66,	0,199,552,4836,24913

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 from FlyBase were aligned against the D. ananassae gneome assembly using Spaln2 with cross-species parameters. Methods The list of genes that aligned to each contig were determined by the best hit in the D. melanogaster blastx track at each genomic locus. mRNA transcripts from each of these genes were aligned against the contig using Spaln2 with cross-species parameters optimized for D. melanogaster: (-Tdromel -yX -yS). 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