ScoringMatrix (BioFSharp) | BioFSharp

ScoringMatrix Module

Namespace: BioFSharp.Algorithm
Assembly: BioFSharp.dll

Contains functions for using the included similarity matrices. These assign a score to every pair of aminoacids/nucleotides and therefore rate the probability of their substitution. The Scoring Matrices are generally used for alignments.

Types

Type	Description
ScoringMatrixAminoAcid	Union case of implemented amino acid scoring matrices with the given reference to its place in the library. Use the "getScoringMatrixAminoAcid" function to obtain a simple mapping function for every amino acid pair
ScoringMatrixNucleotide	Union case of implemented nucleotide scoring matrices with the given reference to its place in the library. Use the "getScoringMatrixNucleotide" function to obtain a simple mapping function for every nucleotide pair

Functions and values

Function or value	Description
`getPrimitiveScoringMatrixNucleotide scoringMatrixType` Full Usage: `getPrimitiveScoringMatrixNucleotide scoringMatrixType` Parameters: scoringMatrixType : `ScoringMatrixNucleotide` Returns: `int[][]`	scoringMatrixType : `ScoringMatrixNucleotide` Returns: `int[][]`
`getScoringMatrixAminoAcid scoringMatrixType` Full Usage: `getScoringMatrixAminoAcid scoringMatrixType` Parameters: scoringMatrixType : `ScoringMatrixAminoAcid` Returns: `AminoAcidSymbol -> AminoAcidSymbol -> int`	creates a scoring function for amino acids out of a scoring matrix scoringMatrixType : `ScoringMatrixAminoAcid` Returns: `AminoAcidSymbol -> AminoAcidSymbol -> int`
`getScoringMatrixNucleotide scoringMatrixType` Full Usage: `getScoringMatrixNucleotide scoringMatrixType` Parameters: scoringMatrixType : `ScoringMatrixNucleotide` Returns: `Nucleotide -> Nucleotide -> int`	creates a scoring function for nucleotides out of a scoring matrix scoringMatrixType : `ScoringMatrixNucleotide` Returns: `Nucleotide -> Nucleotide -> int`