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

Database: DereCAF1 Primary Table: DmelTranscriptsBLAT Row Count: 32,147 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	scaffold_1121	`varchar(255)`	values
`chromStart`	273	`int(10) unsigned`	range
`chromEnd`	414	`int(10) unsigned`	range
`name`	His3:CG33815-RA	`varchar(255)`	values
`score`	844	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	273	`int(10) unsigned`	range
`thickEnd`	414	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	141	`longblob`
`chromStarts`	0	`longblob`
`id`	FBtr0091819	`varchar(255)`	values
`description`	FBgn0053815	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	id	description
scaffold_1121	273	414	His3:CG33815-RA	844	-	273	414	1	141	FBtr0091819	FBgn0053815
scaffold_1121	273	414	His3:CG33818-RA	844	-	273	414	1	141	FBtr0091822	FBgn0053818
scaffold_1121	273	414	His3:CG33803-RA	844	-	273	414	1	141	FBtr0091807	FBgn0053803
scaffold_1121	273	414	His3:CG33821-RA	844	-	273	414	1	141	FBtr0091825	FBgn0053821
scaffold_1121	273	414	His3:CG33824-RA	844	-	273	414	1	141	FBtr0091828	FBgn0053824
scaffold_1121	273	414	His3:CG33812-RA	844	-	273	414	1	141	FBtr0091816	FBgn0053812
scaffold_1121	273	414	His3:CG33827-RA	844	-	273	414	1	141	FBtr0091831	FBgn0053827
scaffold_1121	273	414	His3:CG33830-RA	844	-	273	414	1	141	FBtr0091834	FBgn0053830
scaffold_1121	273	414	His3:CG33833-RA	844	-	273	414	1	141	FBtr0091837	FBgn0053833
scaffold_1121	273	414	His3:CG33836-RA	844	-	273	414	1	141	FBtr0091840	FBgn0053836

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. erecta 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. erecta 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