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

Database: DperCAF1 Primary Table: DmelTranscriptsBLAT Row Count: 31,364 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	super_0	`varchar(255)`	values
`chromStart`	34443	`int(10) unsigned`	range
`chromEnd`	46568	`int(10) unsigned`	range
`name`	CG7029-RF	`varchar(255)`	values
`score`	664	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	34774	`int(10) unsigned`	range
`thickEnd`	42842	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	47	`int(11)`	range
`blockSizes`	24,5,17,25,34,69,45,231,51,...	`longblob`
`chromStarts`	0,158,163,204,320,424,523,8...	`longblob`
`id`	FBtr0310037	`varchar(255)`	values
`description`	FBgn0039026	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
super_0	34443	46568	CG7029-RF	664	-	34774	42842	47	24,5,17,25,34,69,45,231,51,225,123,83,33,88,237,53,226,36,48,141,156,72,17,6,120,144,14,117,220,303,72,12,105,27,76,12,43,62,54, ...	0,158,163,204,320,424,523,854,1097,1181,1415,1542,1658,1697,1805,2117,2173,2408,2447,2498,2702,2882,2976,2996,3065,3251,3827,384 ...	FBtr0310037	FBgn0039026
super_0	34443	75931	CG7029-RD	668	-	34774	39999	48	24,5,17,25,34,69,45,33,34,224,51,225,123,83,33,88,237,53,226,36,48,141,156,72,17,6,120,144,14,117,220,303,72,12,105,27,76,12,43, ...	0,158,163,204,320,424,523,667,730,861,1097,1181,1415,1542,1658,1697,1805,2117,2173,2408,2447,2498,2702,2882,2976,2996,3065,3251, ...	FBtr0113271	FBgn0039026
super_0	34443	79145	CG7029-RC	672	-	34774	39999	51	24,5,17,25,34,69,45,33,34,224,51,225,123,83,33,88,237,53,226,36,48,141,156,72,17,6,120,144,14,117,220,303,72,12,105,27,76,12,43, ...	0,158,163,204,320,424,523,667,730,861,1097,1181,1415,1542,1658,1697,1805,2117,2173,2408,2447,2498,2702,2882,2976,2996,3065,3251, ...	FBtr0113270	FBgn0039026
super_0	34443	46568	CG7029-RA	666	-	34774	42842	49	24,5,17,25,34,69,45,33,34,224,51,225,123,83,33,88,237,53,226,36,48,141,156,72,17,6,120,144,14,117,220,303,72,12,105,27,76,12,43, ...	0,158,163,204,320,424,523,667,730,861,1097,1181,1415,1542,1658,1697,1805,2117,2173,2408,2447,2498,2702,2882,2976,2996,3065,3251, ...	FBtr0084312	FBgn0039026
super_0	34443	79145	CG7029-RG	668	-	34774	39999	50	24,5,17,25,34,69,45,33,225,51,225,123,83,33,88,237,53,226,36,48,141,156,72,17,6,120,144,14,117,220,252,72,12,105,27,76,12,43,62, ...	0,158,163,204,320,424,523,667,860,1097,1181,1415,1542,1658,1697,1805,2117,2173,2408,2447,2498,2702,2882,2976,2996,3065,3251,3827 ...	FBtr0310038	FBgn0039026
super_0	34443	79145	CG7029-RI	670	-	34774	39999	51	24,5,17,25,34,69,45,33,34,224,51,225,123,83,33,88,237,53,226,36,48,141,156,72,17,6,120,111,14,117,220,303,72,12,105,27,76,12,43, ...	0,158,163,204,320,424,523,667,730,861,1097,1181,1415,1542,1658,1697,1805,2117,2173,2408,2447,2498,2702,2882,2976,2996,3065,3251, ...	FBtr0344297	FBgn0039026
super_0	53819	79145	Usp12-46-RB	750	-	53819	55120	10	636,42,39,455,21,27,5,33,41,67	0,645,717,898,25037,25144,25176,25182,25216,25259	FBtr0084311	FBgn0039025
super_0	61783	62084	CG13841-RA	632	+	61783	62084	3	21,51,69	0,147,232	FBtr0084316	FBgn0040588
super_0	61783	62084	CG13841-RB	632	+	61783	62084	3	21,51,69	0,147,232	FBtr0346733	FBgn0040588
super_0	63573	65714	Nepl15-RA	462	+	63712	65714	6	42,206,121,180,819,633	0,139,346,488,686,1508	FBtr0084317	FBgn0039024

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. persimilis 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. persimilis 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