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

Database: DsuzGB1 Primary Table: DmelTranscriptsBLAT Row Count: 34,405 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	AWUT01012676	`varchar(255)`	values
`chromStart`	21764	`int(10) unsigned`	range
`chromEnd`	44750	`int(10) unsigned`	range
`name`	Parp1-RB	`varchar(255)`	values
`score`	584	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	21764	`int(10) unsigned`	range
`thickEnd`	44750	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	3	`int(11)`	range
`blockSizes`	331,138,111	`longblob`
`chromStarts`	0,390,22875	`longblob`
`id`	FBtr0113885	`varchar(255)`	values
`description`	FBgn0010247	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
AWUT01012676	21764	44750	Parp1-RB	584	-	21764	44750	3	331,138,111	0,390,22875	FBtr0113885	FBgn0010247
AWUT01013449	8305	60384	IntS3-RA	676	+	8305	60384	11	60,611,634,107,11,781,160,147,124,48,84	0,135,48360,49050,49396,49588,50424,51563,51762,51944,51995	FBtr0111268	FBgn0262117
AWUT01014658	27886	39388	Fis1-RA	672	+	28231	39388	4	36,49,168,111	0,234,340,11391	FBtr0086073	FBgn0039969
AWUT01014658	27886	39388	Fis1-RC	684	+	27886	39388	5	35,69,49,168,111	0,92,234,340,11391	FBtr0273208	FBgn0039969
AWUT01014658	27886	39391	Fis1-RD	676	+	28231	39391	4	36,49,168,114	0,234,340,11391	FBtr0273209	FBgn0039969
AWUT01014658	27886	39391	Fis1-RE	686	+	27886	39391	5	35,69,49,168,114	0,92,234,340,11391	FBtr0273210	FBgn0039969
AWUT01014658	27886	39391	Fis1-RF	666	+	28231	39391	4	39,78,168,114	0,84,340,11391	FBtr0273211	FBgn0039969
AWUT01014658	28226	39388	Fis1-RG	680	+	28231	39388	2	168,111	0,11051	FBtr0345012	FBgn0039969
AWUT01014734	1654	21021	CG42784-RD	846	+	3205	19765	49	133,74,18,128,53,196,30,15,11,54,110,16,30,74,33,15,5,80,23,145,109,199,179,160,77,145,105,72,166,57,14,42,91,77,111,14,11,67,47 ...	0,133,282,321,456,550,746,801,825,863,945,1059,1080,1184,1258,1326,1341,1351,1436,1550,14697,15565,15826,16071,17032,17147,17340 ...	FBtr0347400	FBgn0263354
AWUT01014734	1654	21021	CG42784-RJ	848	+	3205	19765	50	133,74,18,128,53,196,30,15,11,54,110,16,30,74,33,15,5,80,23,145,61,108,199,179,160,77,145,105,72,166,57,14,42,91,77,111,14,11,67 ...	0,133,282,321,456,550,746,801,825,863,945,1059,1080,1184,1258,1326,1341,1351,1436,1550,3378,14698,15565,15826,16071,17032,17147, ...	FBtr0347401	FBgn0263354

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. suzukii 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. suzukii 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

Methods

References