Schema for Augustus - Augustus Gene Predictions

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Schema for Augustus - Augustus Gene Predictions

Database: DanaCAF1 Primary Table: augustus Row Count: 12,881 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_0.g24.t1	`varchar(255)`	values
`chrom`	scaffold_0	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	0	`int(10) unsigned`	range
`txEnd`	346	`int(10) unsigned`	range
`cdsStart`	0	`int(10) unsigned`	range
`cdsEnd`	346	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	0,157,	`longblob`
`exonEnds`	96,346,	`longblob`
`score`	0	`int(11)`	range
`name2`	scaffold_0.g24	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	scaffold_0.g24.t1	scaffold_0	+	0	346	0	346	2	0,157,	96,346,	0	scaffold_0.g24	unk	unk	0,0,
585	scaffold_10296.g78.t1	scaffold_10296	+	265	1246	265	1246	2	265,970,	590,1246,	0	scaffold_10296.g78	unk	unk	0,1,
585	scaffold_10480.g97.t1	scaffold_10480	-	803	1092	803	1092	2	803,1083,	926,1092,	0	scaffold_10480.g97	unk	unk	0,0,
585	scaffold_10492.g77.t1	scaffold_10492	+	58	518	58	518	2	58,341,	191,518,	0	scaffold_10492.g77	unk	unk	2,0,
585	scaffold_10550.g14.t1	scaffold_10550	+	181	1002	181	1002	1	181,	1002,	0	scaffold_10550.g14	unk	unk	0,
585	scaffold_10575.g6.t1	scaffold_10575	-	128	1053	128	1053	3	128,401,726,	345,664,1053,	0	scaffold_10575.g6	unk	unk	2,0,0,
585	scaffold_10575.g7.t1	scaffold_10575	-	1126	4991	1126	4991	2	1126,4766,	1792,4991,	0	scaffold_10575.g7	unk	unk	0,0,
585	scaffold_11114.g27.t1	scaffold_11114	+	0	966	0	966	1	0,	966,	0	scaffold_11114.g27	unk	unk	0,
585	scaffold_11116.g63.t1	scaffold_11116	+	0	1375	0	1375	1	0,	1375,	0	scaffold_11116.g63	unk	unk	2,
585	scaffold_11119.g18.t1	scaffold_11119	+	0	499	0	499	1	0,	499,	0	scaffold_11119.g18	unk	unk	2,

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. ananassae genome assembly, as well as splice junction predictions and assembled transcripts derived from D. ananassae 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.