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|**`-out_type`**| Output type. Either **'ascii'** (default), which will write single file for each entry in input or **'h5'** which will generate single hdf5 file storing all predictions. |
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|**`-out_filename`**| Works with **"-out_type h5"** option and specifies the hdf5 output filename Overrides the **-out_path** if specified. |
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|**`-min_residue_score`**| Number from range <0,1>. If passed return sequences which have at least one residue with greater score |
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|**`-min_segment_score`**| Number greater than 0. If passed return sequences which have segment of length at least **-min_segment_length**|
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|**`-min_segment_length`**| Number greater than 0. If passed return sequences which have segment of length at least **-min_segment_length**|
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PSSM filenames should be based on the identifiers in the fasta file (only alphanumeric characters and '_'). For example if a fasta sequence is as follows:
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