Schema for D. virilis Assembled Proteins - Assembled Proteins from modENCODE D. virilis RNA-Seq

Database: DmojImproved Primary Table: dvir_asm_proteins Row Count: 90,279

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	72630	`int(10) unsigned`	range
`chromEnd`	74508	`int(10) unsigned`	range
`name`	Dvir_cfl_males_00000434_84938	`varchar(255)`	values
`score`	428	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	72630	`int(10) unsigned`	range
`thickEnd`	74508	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	4	`int(10) unsigned`	range
`blockSizes`	86,269,154,16,	`longblob`
`chromStarts`	0,301,618,1862	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	improved_6498	72630	74508	Dvir_cfl_males_00000434_84938	428	-	72630	74508	4	86,269,154,16,	0,301,618,1862
587	improved_6498	378559	379615	Dvir_cfl_females_00021405_84507	440	+	378559	379615	2	15,801,	0,255
587	improved_6498	378559	379615	Dvir_cfl_males_00024546_106552	440	+	378559	379615	2	15,801,	0,255
587	improved_6498	386506	387698	Dvir_cem_SRR166837_45710_2_2_22251	934	-	386506	387698	3	2,554,419,	0,125,773
587	improved_6498	386506	389076	Dvir_cfl_males_00014122_97065	927	-	386506	389076	4	679,1434,90,146,	0,773,2275,2424
587	improved_6498	386506	389076	Dvir_cfl_females_00012412_74523	927	-	386506	389076	4	679,1434,90,146,	0,773,2275,2424
587	improved_6498	386506	388798	Dvir_cem_SRR166836_35598_0_2_5657	920	-	386506	388798	3	679,1434,17,	0,773,2275
587	improved_6498	386506	389076	Dvir_cem_SRR166836_35598_0_3_5659	927	-	386506	389076	4	679,1434,90,146,	0,773,2275,2424
587	improved_6498	386701	387698	Dvir_cem_SRR768440_43597_1_1_52382	941	-	386701	387698	2	484,419,	0,578
587	improved_6498	386701	387698	Dvir_cem_SRR768440_43597_1_2_52384	941	-	386701	387698	2	484,419,	0,578

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

D. virilis Assembled Proteins (dvir_asm_proteins) Track Description


	Description RNA-seq reads generated by the modENCODE project for D. virilis were mapped against the D. virilis genome using TopHat2 and predicted transcripts are assembled using Cufflinks and CEM. Coding regions within the predicted transcripts are identified using TransDecoder. This collection of coding regions are aligned against the D. mojavensis genome using blastx followed by Spaln2. Methods Candidate coding regions in the collection of assembled D. virilis transcripts were identified using TransDecoder using the following parameters: -m 50, --search_pfam Pfam-A.hmm. The collection of predicted D. virilis proteins were initially mapped against the D. mojavensis genome using BLASTX to identify regions of similarity. Spaln2 is then used to re-align each protein against their corresponding region with cross-species parameters optimized for D. melanogaster: (-Tdromel -yX -yS). References Hass B. TransDecoder (Finding Coding Regions Within Transcripts). Iwata H., and Gotoh, O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln2 that incorporates additional species-specific features. Nucleic Acids Research. 2012, 109 The RNA-Seq data were submitted by the modENCODE project. The original RNA-Seq dataset can be obtained from the NCBI GEO database under the accession number GSE28078.

Description