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

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

Database: DmojImproved Primary Table: asm_proteins Row Count: 89,363

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	108969	`int(10) unsigned`	range
`chromEnd`	109302	`int(10) unsigned`	range
`name`	Dmoj_cfl_females_00000234_5...	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	108969	`int(10) unsigned`	range
`thickEnd`	109302	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	333,	`longblob`
`chromStarts`	0	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts
585	improved_6498	108969	109302	Dmoj_cfl_females_00000234_55191	1000	-	108969	109302	0	1	333,	0
586	improved_6498	142100	142700	Dmoj_cfl_males_00000258_72262	1000	-	142100	142700	0	1	600,	0
586	improved_6498	142760	143096	Dmoj_cfl_males_00000258_72261	1000	-	142760	143096	0	1	336,	0
586	improved_6498	215866	216808	Dmoj_cfl_females_00000240_55192	1000	-	215866	216808	0	1	942,	0
586	improved_6498	217807	218170	Dmoj_cfl_females_00000241_55193	1000	-	217807	218170	0	1	363,	0
586	improved_6498	218393	218606	Dmoj_cfl_females_00000241_55194	1000	-	218393	218606	0	1	213,	0
586	improved_6498	255953	257055	Dmoj_cfl_males_00022483_94355	878	-	255953	257055	0	2	38,1064,	0,38
587	improved_6498	309820	311062	Dmoj_cfl_males_00000262_72263	992	+	309820	311062	0	1	1242,	0
587	improved_6498	316641	319733	Dmoj_cfl_males_00000003_71972	410	+	316641	319733	0	3	333,31,266,	0,851,2826
587	improved_6498	373749	374889	Dmoj_cfl_males_00000265_72265	1000	+	373749	374889	0	1	1140,	0

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

D. mojavensis Assembled Proteins (asm_proteins) Track Description


	Description RNA-seq reads generated by the modENCODE project for D. mojavensis were mapped against the D. mojavensis 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. mojavensis transcripts were identified using TransDecoder using the following parameters: -m 50, --search_pfam Pfam-A.hmm. The collection of predicted D. mojavensis 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 same-species parameters optimized for D. melanogaster: (-Tdromel -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.