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

Database: DobsGB1 Primary Table: DmelTranscriptsBLAT Row Count: 31,590 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	BDQP01000001	`varchar(255)`	values
`chromStart`	11216	`int(10) unsigned`	range
`chromEnd`	32835	`int(10) unsigned`	range
`name`	Ser-RB	`varchar(255)`	values
`score`	714	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	14011	`int(10) unsigned`	range
`thickEnd`	32224	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	30	`int(11)`	range
`blockSizes`	17,53,49,66,83,117,190,55,3...	`longblob`
`chromStarts`	0,17,83,2765,3024,6988,7752...	`longblob`
`id`	FBtr0344121	`varchar(255)`	values
`description`	FBgn0004197	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
BDQP01000001	11216	32835	Ser-RB	714	+	14011	32224	30	17,53,49,66,83,117,190,55,316,134,182,61,3,129,56,36,482,32,103,98,369,519,57,755,14,33,21,13,45,57	0,17,83,2765,3024,6988,7752,12075,12455,14697,14969,15445,15951,16699,16872,16931,16985,17627,17758,17933,19101,19559,20114,2023 ...	FBtr0344121	FBgn0004197
BDQP01000001	11301	32835	Ser-RA	714	+	14011	32224	28	45,66,83,117,190,55,316,134,182,61,3,129,56,36,482,32,103,98,369,519,57,755,14,33,21,13,45,57	0,2680,2939,6903,7667,11990,12370,14612,14884,15360,15866,16614,16787,16846,16900,17542,17673,17848,19016,19474,20029,20147,2092 ...	FBtr0085128	FBgn0004197
BDQP01000001	37919	38885	spn-D-RA	398	-	37919	38885	5	173,124,152,108,114	0,276,463,673,852	FBtr0085116	FBgn0003482
BDQP01000001	39336	39670	CG34293-RA	518	+	39338	39661	2	99,42	0,292	FBtr0112489	FBgn0085322
BDQP01000001	39336	39670	CG34293-RB	518	+	39338	39661	2	99,42	0,292	FBtr0339263	FBgn0085322
BDQP01000001	39779	41247	ppk31-RB	568	-	39779	41247	6	144,105,4,654,207,111	0,206,365,373,1094,1357	FBtr0113383	FBgn0051065
BDQP01000001	42798	43713	CG5909-RA	458	-	42804	43713	6	69,222,86,180,78,135	0,75,331,429,690,780	FBtr0085114	FBgn0039495
BDQP01000001	46003	47348	grass-RA	592	-	46003	47304	5	425,186,50,214,171	0,499,768,883,1174	FBtr0085111	FBgn0039494
BDQP01000001	46003	47348	grass-RB	592	-	46003	47348	5	425,186,50,214,171	0,499,768,883,1174	FBtr0085112	FBgn0039494
BDQP01000001	48147	51877	Men-b-RA	708	-	49657	51877	9	39,36,31,132,297,151,1052,90,57	0,154,1509,1617,1821,2188,2417,3532,3673	FBtr0085110	FBgn0029155

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. obscura 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. obscura 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