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

Database: DmojCAF1 Primary Table: DmelTranscriptsBLAT Row Count: 29,355 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	scaffold_1517	`varchar(255)`	values
`chromStart`	102	`int(10) unsigned`	range
`chromEnd`	228	`int(10) unsigned`	range
`name`	Cpr65Ay-RA	`varchar(255)`	values
`score`	572	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	102	`int(10) unsigned`	range
`thickEnd`	228	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	126	`longblob`
`chromStarts`	0	`longblob`
`id`	FBtr0112466	`varchar(255)`	values
`description`	FBgn0085300	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
scaffold_1517	102	228	Cpr65Ay-RA	572	+	102	228	1	126	0	FBtr0112466	FBgn0085300
scaffold_1657	5587	8691	CG7564-RD	548	+	5587	5588	9	42,237,207,35,16,148,75,1176,23	0,345,693,963,1088,1142,1323,1506,3081	FBtr0345387	FBgn0036734
scaffold_1685	3300	5718	CG7564-RD	608	+	3300	3301	8	200,219,151,55,573,75,356,201	0,305,765,970,1069,1684,1795,2217	FBtr0345387	FBgn0036734
scaffold_1722	1918	4648	eater-RC	286	+	1918	4648	4	138,760,1055,39	0,453,1510,2691	FBtr0310079	FBgn0243514
scaffold_1723	1033	2672	CG31098-RA	526	+	1038	2672	5	201,519,81,214,194	0,207,750,1168,1445	FBtr0084863	FBgn0051098
scaffold_1740	1854	3353	Cyp6a21-RA	468	-	1857	3353	2	422,1021	0,478	FBtr0087456	FBgn0288232
scaffold_1740	1857	5662	Cyp6a9-RB	406	-	1857	5662	3	419,1014,64	0,475,3741	FBtr0300128	FBgn0013771
scaffold_1740	1983	5167	Cyp6w1-RA	250	-	1983	5167	3	69,114,102	0,434,3082	FBtr0085987	FBgn0033065
scaffold_1740	4109	7495	Cyp6a8-RA	274	-	4109	7495	6	360,18,213,18,156,246	0,400,482,2780,2939,3140	FBtr0087455	FBgn0013772
scaffold_1740	4127	7498	Cyp6a19-RA	306	-	4127	7498	5	255,165,15,11,21	0,500,2762,3138,3350	FBtr0087453	FBgn0033979

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. mojavensis 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. mojavensis 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