Schema for Augustus Genes (BUSCO) - Augustus Gene Predictions with BUSCO Training Set
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Database: DereCAF1 Primary Table: augustusBUSCO Row Count: 12,717   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 585 | smallint(5) unsigned | range |
name | scaffold_1230.g19.t1 | varchar(255) | values |
chrom | scaffold_1230 | varchar(255) | values |
strand | - | char(1) | values |
txStart | 0 | int(10) unsigned | range |
txEnd | 638 | int(10) unsigned | range |
cdsStart | 0 | int(10) unsigned | range |
cdsEnd | 638 | int(10) unsigned | range |
exonCount | 3 | int(10) unsigned | range |
exonStarts | 0,250,423, | longblob | |
exonEnds | 193,367,638, | longblob | |
score | 0 | int(11) | range |
name2 | scaffold_1230.g19 | varchar(255) | values |
cdsStartStat | unk | enum('none', 'unk', 'incmpl', 'cmpl') | values |
cdsEndStat | unk | enum('none', 'unk', 'incmpl', 'cmpl') | values |
exonFrames | 2,2,0, | longblob | |
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Sample Rows
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bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | score | name2 | cdsStartStat | cdsEndStat | exonFrames |
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585 | scaffold_1230.g19.t1 | scaffold_1230 | - | 0 | 638 | 0 | 638 | 3 | 0,250,423, | 193,367,638, | 0 | scaffold_1230.g19 | unk | unk | 2,2,0, |
585 | scaffold_1240.g18.t1 | scaffold_1240 | - | 396 | 1412 | 396 | 1412 | 1 | 396, | 1412, | 0 | scaffold_1240.g18 | unk | unk | 2, |
585 | scaffold_1246.g25.t1 | scaffold_1246 | + | 330 | 1113 | 330 | 1113 | 1 | 330, | 1113, | 0 | scaffold_1246.g25 | unk | unk | 0, |
585 | scaffold_1247.g8.t1 | scaffold_1247 | - | 0 | 1233 | 0 | 1233 | 2 | 0,325, | 275,1233, | 0 | scaffold_1247.g8 | unk | unk | 0,1, |
585 | scaffold_1251.g28.t1 | scaffold_1251 | + | 758 | 1475 | 758 | 1475 | 2 | 758,1217, | 1136,1475, | 0 | scaffold_1251.g28 | unk | unk | 0,0, |
585 | scaffold_1255.g6.t1 | scaffold_1255 | + | 115 | 900 | 115 | 900 | 2 | 115,411, | 322,900, | 0 | scaffold_1255.g6 | unk | unk | 0,0, |
585 | scaffold_1259.g10.t1 | scaffold_1259 | - | 0 | 1299 | 0 | 1299 | 2 | 0,993, | 220,1299, | 0 | scaffold_1259.g10 | unk | unk | 2,2, |
585 | scaffold_1260.g7.t1 | scaffold_1260 | + | 0 | 1055 | 0 | 1055 | 1 | 0, | 1055, | 0 | scaffold_1260.g7 | unk | unk | 2, |
585 | scaffold_1264.g31.t1 | scaffold_1264 | + | 153 | 3082 | 153 | 3082 | 2 | 153,2608, | 936,3082, | 0 | scaffold_1264.g31 | unk | unk | 0,0, |
585 | scaffold_1286.g2.t1 | scaffold_1286 | + | 0 | 759 | 0 | 759 | 2 | 0,522, | 467,759, | 0 | scaffold_1286.g2 | unk | unk | 1,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Augustus Genes (BUSCO) (augustusBUSCO) Track Description
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Description
This track shows the gene models from the
Augustus gene predictor using the species-specific parameters estimated from a training set produced by BUSCO.
Methods
The training set used to estimate the species-specific parameters for the Augustus analysis
was produced by BUSCO using the
arthropoda_odb9
dataset.
Transposons remnants identified by RepeatMasker were provided as hints to the Augustus gene predictor.
The following additional parameters were used with the Augustus gene predictor:
--strand=both
--noInFrameStop=true
--gff3=on
--uniqueGeneId=true
--protein=off
--codingseq=off
--introns=off
--stop=off
--cds=on
--singlestrand=false
--UTR=off
--genemodel=partial
References
Stanke M, Waack S.
Gene prediction with a hidden Markov model and a new intron submodel.
Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25.
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM.
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Bioinformatics. 2015 Oct 1;31(19):3210-2.
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