Schema for D. mel Transcripts - BLAT Alignment of D. melanogaster Transcripts

Database: DariGB1 Primary Table: DmelTranscriptsBLAT Row Count: 27,865 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	LSRM01000001	`varchar(255)`	values
`chromStart`	62856	`int(10) unsigned`	range
`chromEnd`	66754	`int(10) unsigned`	range
`name`	Coq8-RA	`varchar(255)`	values
`score`	600	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	62856	`int(10) unsigned`	range
`thickEnd`	66754	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	6	`int(11)`	range
`blockSizes`	553,782,57,105,60,141	`longblob`
`chromStarts`	0,1550,3232,3373,3619,3757	`longblob`
`id`	FBtr0073697	`varchar(255)`	values
`description`	FBgn0052649	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
LSRM01000001	62856	66754	Coq8-RA	600	-	62856	66754	6	553,782,57,105,60,141	0,1550,3232,3373,3619,3757	FBtr0073697	FBgn0052649
LSRM01000001	68154	69447	CG17486-RB	288	+	68154	69447	5	63,129,147,153,72	0,522,807,987,1221	FBtr0299924	FBgn0032997
LSRM01000001	70820	71498	Flad1-RA	480	-	70820	71498	3	68,171,309	0,114,369	FBtr0073695	FBgn0030431
LSRM01000001	70820	71498	Flad1-RB	480	-	70820	71498	3	68,171,309	0,114,369	FBtr0073696	FBgn0030431
LSRM01000001	70931	71486	Flad2-RA	356	-	70931	71486	2	166,42	0,513	FBtr0080501	FBgn0032522
LSRM01000001	72854	75626	CG4404-RA	642	-	72854	75626	4	129,17,167,154	0,814,918,2618	FBtr0073694	FBgn0030432
LSRM01000001	76821	77268	mRpL49-RA	456	+	76821	77268	1	447	0	FBtr0073691	FBgn0030433
LSRM01000001	76821	77268	mRpL49-RB	456	+	76821	77268	1	447	0	FBtr0343185	FBgn0030433
LSRM01000001	78353	79196	Brms1-RA	644	-	78353	79195	4	257,238,78,92	0,326,646,751	FBtr0073693	FBgn0030434
LSRM01000001	79816	81008	CG4645-RA	554	+	79816	81008	7	48,64,66,216,207,93,180	0,59,159,285,577,860,1012	FBtr0073692	FBgn0030435

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

D. mel Transcripts (DmelTranscriptsBLAT) Track Description


	Description D. melanogaster transcripts annotated by FlyBase were aligned against the D. arizonae genome assembly using a translated BLAT search. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. melanogaster transcripts were mapped against the D. arizonae genome assembly using BLAT with the following parameters: `-q=rnax -t=dnax -mask=lower` The transcript alignments are analyzed by pslReps to identify the best alignments within the genome assembly that have a minimum alignment ratio of 0.25 (`-minAli=0.25`). The alignments are then filtered by pslCDnaFilter using the following parameters: -minId=0.35 -minCover=0.15 -localNearBest=0.010 -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap References Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.

Description