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

Database: DkikGB2 Primary Table: DmelTranscriptsBLAT Row Count: 30,960 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	AFFH02000335	`varchar(255)`	values
`chromStart`	35226	`int(10) unsigned`	range
`chromEnd`	35498	`int(10) unsigned`	range
`name`	CG4783-RA	`varchar(255)`	values
`score`	544	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	35226	`int(10) unsigned`	range
`thickEnd`	35458	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(11)`	range
`blockSizes`	102,100	`longblob`
`chromStarts`	0,172	`longblob`
`id`	FBtr0083823	`varchar(255)`	values
`description`	FBgn0038756	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
AFFH02000335	35226	35498	CG4783-RA	544	-	35226	35458	2	102,100	0,172	FBtr0083823	FBgn0038756
AFFH02000335	35226	35498	CG4783-RB	544	-	35226	35458	2	102,100	0,172	FBtr0344285	FBgn0038756
AFFH02000335	41920	42076	CG46042-RC	284	+	41920	42076	1	156	0	FBtr0475137	FBgn0267709
AFFH02000335	48676	58947	Hs6st-RA	774	+	48676	58251	12	112,13,168,549,187,172,27,41,88,33,95,42	0,112,153,384,992,9441,9633,9680,9721,9960,10107,10229	FBtr0083846	FBgn0038755
AFFH02000335	48676	59083	Hs6st-RB	770	+	48676	58251	13	112,13,168,549,187,172,27,41,88,33,95,42,65	0,112,153,384,992,9441,9633,9680,9721,9960,10107,10229,10342	FBtr0335240	FBgn0038755
AFFH02000335	53129	55657	mira-RA	732	+	53148	55654	7	117,204,860,861,177,51,93	0,155,362,1268,2132,2309,2435	FBtr0083847	FBgn0021776
AFFH02000335	53129	55657	mira-RB	724	+	53148	55654	8	117,204,860,537,234,177,51,93	0,155,362,1268,1895,2132,2309,2435	FBtr0083848	FBgn0021776
AFFH02000335	53129	55657	mira-RC	726	+	53148	55654	8	117,204,860,537,252,177,51,93	0,155,362,1268,1877,2132,2309,2435	FBtr0335243	FBgn0021776
AFFH02000335	60017	62209	CG4459-RA	636	+	60110	62179	6	30,528,155,294,303,581	0,93,683,928,1250,1611	FBtr0083849	FBgn0038753
AFFH02000335	64918	67887	CG4462-RA	642	+	64918	67887	5	65,583,507,141,401	0,68,719,2366,2568	FBtr0083850	FBgn0038752

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. kikkawai 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. kikkawai 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