Schema for Augustus - Augustus Gene Predictions

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Schema for Augustus - Augustus Gene Predictions

Database: DsuzGB1 Primary Table: augustus Row Count: 19,863

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	augustus_AWUT01012676.g825.t1	`varchar(255)`	values
`chrom`	AWUT01012676	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	21499	`int(10) unsigned`	range
`txEnd`	50905	`int(10) unsigned`	range
`cdsStart`	21656	`int(10) unsigned`	range
`cdsEnd`	44753	`int(10) unsigned`	range
`exonCount`	5	`int(10) unsigned`	range
`exonStarts`	21499,21763,22150,44639,50849,	`longblob`
`exonEnds`	21678,22088,22292,44927,50905,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	augustus_AWUT01012676.g825.t1	AWUT01012676	-	21499	50905	21656	44753	5	21499,21763,22150,44639,50849,	21678,22088,22292,44927,50905,
585	augustus_AWUT01012676.g825.t2	AWUT01012676	-	21499	50905	21656	44753	5	21499,21763,22150,44639,50849,	21678,22097,22292,44927,50905,
585	augustus_AWUT01013263.g1564.t1	AWUT01013263	+	17655	47940	17693	47725	2	17655,47376,	17725,47940,
585	augustus_AWUT01013449.g142.t2	AWUT01013449	+	5515	60761	8278	60564	15	5515,8151,8440,8797,56665,57355,57606,57866,58260,58667,58731,59940,60065,60249,60492,	5612,8365,8617,9051,56963,57548,57815,58140,58355,58676,58889,60013,60191,60438,60761,
585	augustus_AWUT01013449.g142.t1	AWUT01013449	+	5515	60761	8278	60564	16	5515,8151,8440,8797,56665,57111,57355,57606,57866,58260,58667,58731,59940,60065,60249,60492,	5612,8365,8617,9051,56757,57299,57548,57815,58140,58355,58676,58889,60013,60191,60438,60761,
585	augustus_AWUT01013449.g143.t1	AWUT01013449	+	63005	66458	63374	65800	5	63005,63272,63579,65743,65876,	63217,63429,63683,65823,66458,
585	augustus_AWUT01013449.g144.t1	AWUT01013449	-	68326	68735	68398	68692	1	68326,	68735,
585	augustus_AWUT01014088.g1542.t1	AWUT01014088	-	31124	31175	31124	31150	1	31124,	31175,
585	augustus_AWUT01014658.g1209.t1	AWUT01014658	+	23775	32115	27877	32024	6	23775,27823,27979,28120,28226,31970,	23852,27922,28047,28169,28394,32115,
585	augustus_AWUT01014658.g1209.t2	AWUT01014658	+	23775	39552	27877	39394	6	23775,27823,27979,28120,28226,39277,	23852,27922,28047,28169,28394,39552,

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

Augustus (augustus) Track Description


	Description This track shows the gene predictions from the Augustus program. The predictions are based on hints provided by the SPALN alignments of D. melanogaster proteins against the D. suzukii genome assembly, as well as splice junction predictions and assembled transcripts derived from D. suzukii RNA-Seq data. References Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. doi: 10.1093/bioinformatics/btn013. Iwata H, Gotoh O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Res. 2012 Nov 1;40(20):e161. doi: 10.1093/nar/gks708. Haas BJ et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug;8(8):1494-512. Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol. 2019 Dec 16;20(1):278.