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Table 1 Adjustable parameters for model scoring and read island assembly

From: SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

Parameter Default value
Maximum homolog count 3
Acceptable intron donor-acceptor pairs GT-AG, GC-AG, AT-AC
Minimum intron length 10
Maximum intron length 2000
Minimum protein length 150 amino acids
Low median coverage cutoff 10
Low coverage penalty factor 0.6
Acceptable range of exon coverage depth 0.15 to 3 × transcript median depth
Maximum length of low coverage run 10
Low coverage run threshold 0.05 × transcript mean depth
Maximum N count per transcript 8
Threshold score for “Matches RNA-Seq data” status 0.5
Selection pseudoscore 0.0001
Read island minimum cover depth 3
Read island minimum length 100