Average MaxZ Score Calculator
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
Installation
To Install:
In the same directory that setup.py exists in, type:
pip install .
To Uninstall:
pip uninstall averagemaxz
Usage
maxz [-h/--help] -a/--alignment ALIGNMENT -s {protein,nucleotide} -m/--matrix MATRIX -d/--distribution DISTRIBUTION -c/--convert {yes,no}
Arguments
-h/--help (optional)
- show help message and exit.
-a/--alignment ALIGNMENT
-
Enter alignment file.
-
NOTE: Make sure file follows FASTA formatting.
-s/--symbol {protein,nucleotide}
- Enter type of alignment being inputted.
-m/--matrix MATRIX
-
Select similarity matrix.
-
PRESETS: blosum62, blosum90, blosum100, pam100, pam250, binary.
-
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.
-
NOTE: Binary matrices ignore any similarities among disparate symbols.
-
NOTE: Nucelotide alignments that are not converted must use a binary matrix.
-d/--distribution DISTRIBUTION
-
Select sequences to define the background distribution.
-
PRESETS: self, swiss-prot
-
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).
-
NOTE: If self is chosen the sequences of the inputted alignment file will be used
-c/--convert {yes,no}
-
Convert nucleotide alignment to protein alignment?
-
NOTE: Sequences in alignment must be of equal length to convert.
-
NOTE: First open reading frame is used for conversion.