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

Database: DbiaGB2 Primary Table: DmelTranscriptsBLAT Row Count: 31,291 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	AFFD02000037	`varchar(255)`	values
`chromStart`	2876	`int(10) unsigned`	range
`chromEnd`	4053	`int(10) unsigned`	range
`name`	Pcmt-RC	`varchar(255)`	values
`score`	728	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	2934	`int(10) unsigned`	range
`thickEnd`	3907	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	4	`int(11)`	range
`blockSizes`	114,137,411,147	`longblob`
`chromStarts`	0,175,565,1030	`longblob`
`id`	FBtr0339519	`varchar(255)`	values
`description`	FBgn0086768	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
AFFD02000037	2876	4053	Pcmt-RC	728	+	2934	3907	4	114,137,411,147	0,175,565,1030	FBtr0339519	FBgn0086768
AFFD02000037	2876	4053	Pcmt-RA	730	+	2934	3990	4	114,137,405,147	0,175,565,1030	FBtr0078758	FBgn0086768
AFFD02000037	5335	7009	mia-RA	458	+	5335	7009	6	234,243,45,114,111,210	0,336,744,792,1305,1464	FBtr0089313	FBgn0014342
AFFD02000037	5335	7009	mia-RB	458	+	5335	7009	6	234,243,45,114,111,210	0,336,744,792,1305,1464	FBtr0300009	FBgn0014342
AFFD02000037	5335	7009	mia-RC	458	+	5335	7009	6	234,243,45,114,111,210	0,336,744,792,1305,1464	FBtr0346136	FBgn0014342
AFFD02000037	7829	16610	CG2519-RA	746	+	9188	15215	30	53,84,214,208,72,318,1214,360,458,99,301,285,165,213,15,27,13,7,32,14,79,57,25,24,18,122,15,55,31,25	0,53,1359,1631,2293,2955,3431,4736,5152,5663,5822,6184,6534,7179,7447,7480,7644,7686,7698,7734,7812,7893,7973,7998,8070,8371,855 ...	FBtr0078761	FBgn0037336
AFFD02000037	7829	16610	CG2519-RB	742	+	9188	15215	29	53,84,214,208,318,1214,360,458,99,301,285,165,213,15,27,13,7,32,14,79,57,25,24,18,122,15,55,31,25	0,53,1359,1631,2955,3431,4736,5152,5663,5822,6184,6534,7179,7447,7480,7644,7686,7698,7734,7812,7893,7973,7998,8070,8371,8552,857 ...	FBtr0078762	FBgn0037336
AFFD02000037	7829	16610	CG2519-RC	742	+	9188	15215	36	53,110,30,21,16,5,40,27,47,214,208,318,1214,360,458,99,301,285,165,213,15,27,13,7,32,14,79,57,25,24,18,122,15,55,31,25	0,53,163,196,247,264,276,318,345,1359,1631,2955,3431,4736,5152,5663,5822,6184,6534,7179,7447,7480,7644,7686,7698,7734,7812,7893, ...	FBtr0336771	FBgn0037336
AFFD02000037	17187	21741	Itpr-RA	754	-	17690	21741	13	39,32,116,14,5,39,576,428,165,173,121,195,1974	0,69,127,247,262,268,492,1119,1606,1828,2139,2320,2580	FBtr0078686	FBgn0010051
AFFD02000037	17187	21741	Itpr-RB	754	-	17690	21741	13	39,32,116,14,5,39,576,428,165,173,121,195,1974	0,69,127,247,262,268,492,1119,1606,1828,2139,2320,2580	FBtr0078687	FBgn0010051

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. biarmipes 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. biarmipes 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