Input: Multiple Sequence Alignment (MSA) in FASTA file format.
Output: Average maxZ score of the MSA.
Calculates the average maxZ score across all the positions of a multiple sequence alignment, resulting in a statistic which gauges the polymorphic extent of the sequences in that alignment. This score may be useful for the rank ordering of a defined group of MSA's.
The maxZ score is a statistical measure which quantifies the degree of conservation at a given alignment position (Ahola, Aittokallio, Vinhinen, & Uusipaikka, 2006).
Ahola, V., Aittokallio, T., Vihinen, M., & Uusipaikka, E. (2006). A statistical score for assessing the quality of multiple sequence alignments. BMC Bioinformatics, 7(1), 484. doi:10.1186/1471-2105-7-484
In the same directory that setup.py exists in, type:
pip install .
pip uninstall averagemaxz
maxz [-h/--help] -a/--alignment ALIGNMENT -s {protein,nucleotide} -m/--matrix MATRIX -d/--distribution DISTRIBUTION -c/--convert {yes,no}
- show help message and exit.
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Enter alignment file.
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NOTE: Make sure file follows FASTA formatting.
- Enter type of alignment being inputted.
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Select similarity matrix.
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PRESETS: blosum62, blosum90, blosum100, pam100, pam250, binary.
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NOTE: If a preset is not chosen the program will assume you are loading a file. Make sure the file you load follows the standard format set by PAM and BLOSUM.
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NOTE: Binary matrices ignore any similarities among disparate symbols.
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NOTE: Nucelotide alignments that are not converted must use a binary matrix.
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Select sequences to define the background distribution.
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PRESETS: self, swiss-prot
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NOTE: If a preset is not chosen the program will assume you are loading a file. Make sure any file you load follows FASTA formatting and is of the same symbol type (protein or nucleotide).
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NOTE: If self is chosen the sequences of the inputted alignment file will be used
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Convert nucleotide alignment to protein alignment?
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NOTE: Sequences in alignment must be of equal length to convert.
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NOTE: First open reading frame is used for conversion.