Schema for Augustus - Augustus Gene Predictions

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Schema for Augustus - Augustus Gene Predictions

Database: DbipGB2 Primary Table: augustus Row Count: 18,249

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	augustus_AFFE02000126.g8.t1	`varchar(255)`	values
`chrom`	AFFE02000126	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	5635	`int(10) unsigned`	range
`txEnd`	7306	`int(10) unsigned`	range
`cdsStart`	5753	`int(10) unsigned`	range
`cdsEnd`	7122	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	5635,6615,6912,	`longblob`
`exonEnds`	6424,6862,7306,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	augustus_AFFE02000126.g8.t1	AFFE02000126	+	5635	7306	5753	7122	3	5635,6615,6912,	6424,6862,7306,
585	augustus_AFFE02000144.g14.t1	AFFE02000144	+	4937	5918	4937	5405	1	4937,	5918,
585	augustus_AFFE02000172.g17.t1	AFFE02000172	+	34	25118	65	24932	10	34,583,2113,18945,19120,20594,22460,23706,24557,24720,	447,1162,2304,19055,19373,20893,22736,23841,24658,25118,
585	augustus_AFFE02000172.g17.t2	AFFE02000172	+	34	25118	65	24932	10	34,583,2113,18945,19120,20594,22457,23706,24557,24720,	447,1162,2304,19055,19373,20893,22736,23841,24658,25118,
585	augustus_AFFE02000172.g18.t1	AFFE02000172	+	30835	31468	31003	31402	2	30835,30987,	30888,31468,
585	augustus_AFFE02000172.g19.t1	AFFE02000172	+	67105	68189	67372	68089	1	67105,	68189,
585	augustus_AFFE02000172.g20.t1	AFFE02000172	+	68355	68606	68422	68606	1	68355,	68606,
585	augustus_AFFE02000235.g23.t1	AFFE02000235	-	15471	17065	15471	16726	3	15471,15866,16214,	15698,16133,17065,
585	augustus_AFFE02000309.g30.t1	AFFE02000309	-	0	1255	134	1180	2	0,328,	275,1255,
585	augustus_AFFE02000339.g32.t1	AFFE02000339	-	0	11305	96	10703	3	0,9452,11278,	249,10727,11305,

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