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

Database: DsimGB2 Primary Table: DmelTranscriptsBLAT Row Count: 31,675 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	CM002910	`varchar(255)`	values
`chromStart`	4183	`int(10) unsigned`	range
`chromEnd`	12635	`int(10) unsigned`	range
`name`	l(2)gl-RC	`varchar(255)`	values
`score`	890	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	5294	`int(10) unsigned`	range
`thickEnd`	11256	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	20	`int(11)`	range
`blockSizes`	123,15,51,120,48,60,24,18,2...	`longblob`
`chromStarts`	0,196,211,342,578,733,836,9...	`longblob`
`id`	FBtr0078170	`varchar(255)`	values
`description`	FBgn0002121	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
CM002910	4183	12635	l(2)gl-RC	890	-	5294	11256	20	123,15,51,120,48,60,24,18,274,109,441,642,107,1192,779,155,45,38,117,36	0,196,211,342,578,733,836,901,967,1304,1675,2190,3397,3561,4811,6988,8149,8253,8298,8416	FBtr0078170	FBgn0002121
CM002910	4183	12636	l(2)gl-RB	890	-	5294	11256	18	123,15,51,120,48,60,24,18,274,109,441,642,107,1192,779,126,117,37	0,196,211,342,578,733,836,901,967,1304,1675,2190,3397,3561,4811,7017,8298,8416	FBtr0078166	FBgn0002121
CM002910	4183	12635	l(2)gl-RF	888	-	5294	9711	19	123,15,51,120,48,60,24,18,274,109,441,642,107,1192,779,126,45,31,27	0,196,211,342,578,733,836,901,967,1304,1675,2190,3397,3561,4811,7017,8149,8253,8425	FBtr0078169	FBgn0002121
CM002910	4183	12636	l(2)gl-RD	888	-	5294	9711	20	123,15,51,120,48,60,24,18,274,109,441,642,107,1192,779,126,45,38,117,37	0,196,211,342,578,733,836,901,967,1304,1675,2190,3397,3561,4811,7017,8149,8253,8298,8416	FBtr0078167	FBgn0002121
CM002910	4183	12636	l(2)gl-RE	888	-	5294	9711	20	123,15,51,120,48,60,24,18,274,109,441,642,107,1192,779,126,45,38,117,37	0,196,211,342,578,733,836,901,967,1304,1675,2190,3397,3561,4811,7017,8149,8253,8298,8416	FBtr0078168	FBgn0002121
CM002910	4183	12636	l(2)gl-RG	892	-	5294	11256	18	123,15,51,120,48,60,24,18,274,109,441,642,107,1192,779,155,117,37	0,196,211,342,578,733,836,901,967,1304,1675,2190,3397,3561,4811,6988,8298,8416	FBtr0306589	FBgn0002121
CM002910	4183	12635	l(2)gl-RA	890	-	5294	11256	22	123,15,51,120,48,60,24,18,274,109,441,642,107,1192,779,155,4,144,45,38,117,36	0,196,211,342,578,733,836,901,967,1304,1675,2190,3397,3561,4811,6988,7903,7920,8149,8253,8298,8416	FBtr0078171	FBgn0002121
CM002910	4183	12636	l(2)gl-RH	892	-	5294	11256	18	123,15,51,120,48,60,24,18,274,109,441,642,107,1192,779,155,117,37	0,196,211,342,578,733,836,901,967,1304,1675,2190,3397,3561,4811,6988,8298,8416	FBtr0306590	FBgn0002121
CM002910	4183	12636	l(2)gl-RI	890	-	5294	11256	20	123,15,51,120,48,60,24,18,274,109,441,642,107,1192,779,155,45,38,117,37	0,196,211,342,578,733,836,901,967,1304,1675,2190,3397,3561,4811,6988,8149,8253,8298,8416	FBtr0306591	FBgn0002121
CM002910	4183	12636	l(2)gl-RJ	890	-	5294	11256	21	123,15,51,120,48,60,24,18,274,109,441,642,107,1192,779,155,144,45,38,117,37	0,196,211,342,578,733,836,901,967,1304,1675,2190,3397,3561,4811,6988,7920,8149,8253,8298,8416	FBtr0306592	FBgn0002121

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. simulans 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. simulans 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