ClusterFind is the main method of the iPAC package. It identifies clusters of mutated amino acids while taking into account the protein structure.
● Data Source:
BioConductor
● Keywords: Amino Acids, Clusters, Mutations
● Alias: ClusterFind
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Plot.Protein.Linear creates a visual representation of the protein reordering by showing the protein in linear form and setting the color based upon the remapped amino acid position.
● Data Source:
BioConductor
● Keywords: Amino Acids, Mutations, Order
● Alias: Plot.Protein.Linear
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Reads a FASTA (or similarly formatted) file and returns all the amino acids as a list.
● Data Source:
BioConductor
● Keywords: Amino Acids, FASTA
● Alias: get.AASeq
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This function reads a CIF file to extract the names and (x,y,z) coordinates of each residue. It then performs a pairwise alignment to convert the amino acid ordering in the CIF file to the canonical ordering specified by the FASTA file. The first element in the returned list, $Positions, is the positions matrix required by the ClusterFind method.
● Data Source:
BioConductor
● Keywords: Amino Acids, CIF, Positions
● Alias: get.AlignedPositions
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This function reads a CIF file to extract the names and (x,y,z) coordinates of each residue. Then, the information within the CIF file itself is used to identify the canonical position for each amino acid.
● Data Source:
BioConductor
● Keywords: Amino Acids, CIF, Positions
● Alias: get.Positions
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get.Remapped.Order returns the reordering of the culled mutation matrix using the remapper of choice (linear vs MDS).
● Data Source:
BioConductor
● Keywords: Amino Acids, Mutations, Order
● Alias: get.Remapped.Order
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This function takes in the 3 letter amino acid representation and returns the 1 letter representation.
● Data Source:
BioConductor
● Keywords: Amino Acids
● Alias: get.SingleLetterCode
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This package finds mutation clusters on the amino acid level while taking into acount the protein structure.
● Data Source:
BioConductor
● Keywords: package
● Alias: iPAC, iPAC-package
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This runs the clustering algorithm developed by Ye. et. al on the original linear protein.
● Data Source:
BioConductor
● Keywords: NMC
● Alias: nmc
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