19 lines
1.1 KiB
Plaintext
19 lines
1.1 KiB
Plaintext
Pyrodigal is a Python module that provides bindings to Prodigal using Cython.
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Features:
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The library now features everything from the original Prodigal CLI:
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* run mode selection: Choose between single mode, using a training sequence to
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count nucleotide hexamers, or metagenomic mode, using pre-trained data from
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different organisms (prodigal -p).
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* region masking: Prevent genes from being predicted across regions containing
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unknown nucleotides (prodigal -m).
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* closed ends: Genes will be identified as running over edges if they are larger
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than a certain size, but this can be disabled (prodigal -c).
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* training configuration: During the training process, a custom translation
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table can be given (prodigal -g), and the Shine-Dalgarno motif search can be
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forcefully bypassed (prodigal -n)
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* output files: Output files can be written in a format mostly compatible with
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the Prodigal binary, including the protein translations in FASTA format
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(prodigal -a), the gene sequences in FASTA format (prodigal -d), or the
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potential gene scores in tabular format (prodigal -s).
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