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

Database: DtakGB2 Primary Table: DmelTranscriptsBLAT Row Count: 32,054 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	AFFI02000003	`varchar(255)`	values
`chromStart`	10557	`int(10) unsigned`	range
`chromEnd`	32421	`int(10) unsigned`	range
`name`	d4-RA	`varchar(255)`	values
`score`	720	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	10557	`int(10) unsigned`	range
`thickEnd`	32418	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	7	`int(11)`	range
`blockSizes`	380,71,118,118,270,217,187	`longblob`
`chromStarts`	0,460,534,655,20355,21415,2...	`longblob`
`id`	FBtr0086082	`varchar(255)`	values
`description`	FBgn0033015	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
AFFI02000003	10557	32421	d4-RA	720	-	10557	32418	7	380,71,118,118,270,217,187	0,460,534,655,20355,21415,21677	FBtr0086082	FBgn0033015
AFFI02000003	10557	32421	d4-RC	720	-	10557	32418	7	380,71,118,118,264,217,187	0,460,534,655,20361,21415,21677	FBtr0086083	FBgn0033015
AFFI02000003	10557	31182	d4-RB	742	-	10557	31154	5	380,71,118,118,270	0,460,534,655,20355	FBtr0111115	FBgn0033015
AFFI02000003	10557	32421	d4-RD	720	-	10557	32418	7	380,71,118,118,267,217,187	0,460,534,655,20358,21415,21677	FBtr0335258	FBgn0033015
AFFI02000003	39459	42450	CG3107-RA	602	+	39459	42450	7	434,1035,105,309,168,123,556	0,488,1599,1737,2076,2271,2435	FBtr0086077	FBgn0033005
AFFI02000003	39459	42450	CG3107-RB	602	+	39459	42450	7	434,1035,105,309,168,123,552	0,488,1599,1737,2076,2271,2439	FBtr0086078	FBgn0033005
AFFI02000003	39459	42450	CG3107-RC	602	+	39459	42450	7	434,1035,105,309,168,123,556	0,488,1599,1737,2076,2271,2435	FBtr0111280	FBgn0033005
AFFI02000003	39459	42450	CG3107-RD	602	+	39459	42450	7	434,1035,105,309,168,123,556	0,488,1599,1737,2076,2271,2435	FBtr0345009	FBgn0033005
AFFI02000009	5619	12316	yellow-e-RA	774	+	10233	12297	3	54,824,800	0,4603,5897	FBtr0082757	FBgn0041711
AFFI02000009	15458	17269	yellow-e2-RB	710	+	15458	17120	4	250,1062,18,103	0,607,1689,1708	FBtr0302576	FBgn0038151

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. takahashii 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. takahashii 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