org.biojava.nbio.structure.align.multiple.util

Class MultipleAlignmentTools

java.lang.Object

org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

public class MultipleAlignmentTools
extends Object

Utility functions for working with MultipleAlignment.

Supported functions:

• Obtain the alignment as sequence strings
• Map from sequence alignment position to structure Atom
• Map from sequence alignment position to Block number
• Transform the aligned Atoms of a MultipleAlignment
• Get all the core alignment positions of the alignment
• Calculate the average residue distance of all aligned positions
• Sort Blocks in a MultipleAlignment by a specified row
• Convert a MultipleAlignment to a MultipleSequenceAlignment

Since:

4.1.0

Author:

Spencer Bliven, Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
MultipleAlignmentTools()

Method Summary

Modifier and Type	Method and Description
static Structure	getAlignedStructure(List<Atom[]> atomArrays) Get an artificial Structure containing a different model for every input structure, so that the alignment result can be viewed in Jmol.
static Atom	getAtomForSequencePosition(MultipleAlignment msa, List<Integer> mapSeqToStruct, int str, int sequencePos) Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.
static Matrix	getAverageResidueDistances(List<Atom[]> transformed) The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
static Matrix	getAverageResidueDistances(MultipleAlignment msa) The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
static int	getBlockForSequencePosition(MultipleAlignment multAln, List<Integer> mapSeqToStruct, int sequencePos) Returns the block number of a specified position in the sequence alignment, given the mapping from structure to function.
static List<String>	getBlockSequenceAlignment(MultipleAlignment ma) Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
static List<String>	getBlockSequenceAlignment(MultipleAlignment alignment, List<Integer> mapSeqToStruct) Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
static List<Integer>	getCorePositions(Block block) Calculate a List of alignment indicies that correspond to the core of a Block, which means that all structures have a residue in that positon.
static org.forester.phylogeny.Phylogeny	getHSDMTree(MultipleAlignment msta) Calculate a phylogenetic tree of the MultipleAlignment using dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for distantly related proteins, structure-derived) and the Neighbor Joining algorithm from forester.
static org.forester.phylogeny.Phylogeny	getKimuraTree(MultipleAlignment msta) Calculate a phylogenetic tree of the MultipleAlignment using Kimura distances and the Neighbor Joining algorithm from forester.
static Matrix	getRMSDMatrix(MultipleAlignment msa) Calculate the RMSD matrix of a MultipleAlignment, that is, entry (i,j) of the matrix contains the RMSD between structures i and j.
static List<String>	getSequenceAlignment(MultipleAlignment msa) Calculate the sequence alignment Strings for the whole alignment.
static List<String>	getSequenceAlignment(MultipleAlignment alignment, List<Integer> mapSeqToStruct) Calculate the sequence alignment Strings for the whole alignment.
static org.forester.phylogeny.Phylogeny	getStructuralTree(MultipleAlignment msta) Calculate a phylogenetic tree of the MultipleAlignment using RMSD distances and the Neighbor Joining algorithm from forester.
static void	sortBlocks(List<Block> blocks, int sortedIndex) Sort blocks so that the specified row is in sequential order.
static Structure	toMultimodelStructure(MultipleAlignment multAln, List<Atom[]> transformedAtoms)
static MultipleSequenceAlignment<ProteinSequence,AminoAcidCompound>	toProteinMSA(MultipleAlignment msta) Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues.
static List<Atom[]>	transformAtoms(MultipleAlignment alignment) Transforms atoms according to the superposition stored in the alignment.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MultipleAlignmentTools

public MultipleAlignmentTools()

Method Detail

getSequenceAlignment

public static List<String> getSequenceAlignment(MultipleAlignment alignment,
                                                List<Integer> mapSeqToStruct)

Calculate the sequence alignment Strings for the whole alignment. This method creates a sequence alignment where aligned residues are in uppercase and unaligned residues are in lowercase, thus providing a more compact way to represent the alignment.

Blocks are concatenated in the order returned by MultipleAlignment.getBlocks(), so sequences may not be sequential. Gaps are represented by '-'. Separation between different Blocks is indicated by a gap in all positions, meaning that there is a possible discontinuity.

Parameters:

alignment - input MultipleAlignment

mapSeqToStruct - provides a link from the sequence alignment position to the structure alignment position. Specially designed for the GUI. Has to be initialized previously and will be overwritten.

Returns:

a string for each row in the alignment, giving the 1-letter code for each aligned residue.

getSequenceAlignment

public static List<String> getSequenceAlignment(MultipleAlignment msa)

Calculate the sequence alignment Strings for the whole alignment. This method creates a sequence alignment where aligned residues are in uppercase and unaligned residues are in lowercase, thus providing a more compact way to represent the alignment.

Blocks are concatenated in the order returned by MultipleAlignment.getBlocks(), so sequences may not be sequential. Gaps are represented by '-'. Separation between different Blocks is indicated by a gap in all positions, meaning that there is a possible discontinuity.

Parameters:

alignment - input MultipleAlignment

Returns:

String for each row in the alignment, giving the 1-letter code for each aligned residue.

getBlockSequenceAlignment

public static List<String> getBlockSequenceAlignment(MultipleAlignment alignment,
                                                     List<Integer> mapSeqToStruct)

Calculate the sequence alignment Strings for the alignment Blocks in an alignment. This method creates a sequence alignment where all residues are in uppercase and a residue alone with gaps in all the other structures represents unaligned residues. Because of this latter constraint only the residues within the Blocks are represented, for a more compact alignment. For a sequence alignment of the full protein use getSequenceAlignment(MultipleAlignment).

Blocks are concatenated in the order returned by MultipleAlignment.getBlocks(), so sequences may not be sequential. Gaps between blocks are omitted, while gaps within blocks are represented by '-'. Separation between different Blocks is indicated by a gap in all positions, meaning that there is something unaligned inbetween.

Parameters:

alignment - input MultipleAlignment

mapSeqToStruct - provides a link from the sequence alignment position to the structure alignment position. Specially designed for the GUI. Has to be initialized previously and will be overwritten.

Returns:

a string for each row in the alignment, giving the 1-letter code for each aligned residue.

getBlockSequenceAlignment

public static List<String> getBlockSequenceAlignment(MultipleAlignment ma)

Calculate the sequence alignment Strings for the alignment Blocks in an alignment. This method creates a sequence alignment where all residues are in uppercase and a residue alone with gaps in all the other structures represents unaligned residues. Because of this latter constraint only the residues within the Blocks are represented, for a more compact alignment. For a sequence alignment of the full protein use getSequenceAlignment(MultipleAlignment).

Blocks are concatenated in the order returned by MultipleAlignment.getBlocks(), so sequences may not be sequential. Gaps between blocks are omitted, while gaps within blocks are represented by '-'. Separation between different Blocks is indicated by a gap in all positions, meaning that there is something unaligned inbetween.

Parameters:

alignment - input MultipleAlignment

Returns:

String for each row in the alignment, giving the 1-letter code for each aligned residue.

getAtomForSequencePosition

public static Atom getAtomForSequencePosition(MultipleAlignment msa,
                                              List<Integer> mapSeqToStruct,
                                              int str,
                                              int sequencePos)

Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.

Parameters:

multAln - the MultipleAlignment object from where the sequence alignment has been generated

mapSeqToStruct - the mapping between sequence and structure generated with the sequence alignment

str - the structure index of the alignment (row)

sequencePos - the sequence alignment position (column)

Returns:

Atom the atom in that position or null if there is a gap

getBlockForSequencePosition

public static int getBlockForSequencePosition(MultipleAlignment multAln,
                                              List<Integer> mapSeqToStruct,
                                              int sequencePos)

Returns the block number of a specified position in the sequence alignment, given the mapping from structure to function.

Parameters:

multAln - the MultipleAlignment object from where the sequence alignment has been generated.

mapSeqToStruct - the mapping between sequence and structure generated with the sequence alignment

sequencePos - the position in the sequence alignment (column)

Returns:

int the block index, or -1 if the position is not aligned

getAverageResidueDistances

public static Matrix getAverageResidueDistances(MultipleAlignment msa)

The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.

Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment length.

Parameters:

alignment - MultipleAlignment

Returns:

Matrix containing all average residue distances

getAverageResidueDistances

public static Matrix getAverageResidueDistances(List<Atom[]> transformed)

The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.

Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment length.

Parameters:

transformed - List of Atom arrays containing only the aligned atoms of each structure, or null if there is a gap.

Returns:

Matrix containing all average residue distances. Entry -1 means there is a gap in the position.

transformAtoms

public static List<Atom[]> transformAtoms(MultipleAlignment alignment)

Transforms atoms according to the superposition stored in the alignment.

For each structure in the alignment, returns an atom for each representative atom in the aligned columns, omitting unaligned residues (i.e. an array of length alignment.length() ).

All blocks are concatenated together, so Atoms may not appear in the same order as in their parent structure. If the alignment blocks contain null residues (gaps), then the returned array will also contain null Atoms in the same positions.

Parameters:

alignment - MultipleAlignment

Returns:

List of Atom arrays of only the aligned atoms of every structure (null Atom if a gap position)

getCorePositions

public static List<Integer> getCorePositions(Block block)

Calculate a List of alignment indicies that correspond to the core of a Block, which means that all structures have a residue in that positon.

Parameters:

block - alignment Block

Returns:

List of positions in the core of the alignment

sortBlocks

public static void sortBlocks(List<Block> blocks,
                              int sortedIndex)

Sort blocks so that the specified row is in sequential order. The sort happens in place.

Parameters:

blocks - List of blocks

sortedIndex - Index of the row to be sorted

toProteinMSA

public static MultipleSequenceAlignment<ProteinSequence,AminoAcidCompound> toProteinMSA(MultipleAlignment msta)
                                                                                 throws CompoundNotFoundException

Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues. This method is only valid for protein structure alignments.

Parameters:

msta - Multiple Structure Alignment

Returns:

MultipleSequenceAlignment of protein sequences

Throws:

CompoundNotFoundException

toMultimodelStructure

public static Structure toMultimodelStructure(MultipleAlignment multAln,
                                              List<Atom[]> transformedAtoms)
                                       throws StructureException

Throws:

StructureException

getAlignedStructure

public static final Structure getAlignedStructure(List<Atom[]> atomArrays)
                                           throws StructureException

Get an artificial Structure containing a different model for every input structure, so that the alignment result can be viewed in Jmol. The Atoms have to be rotated beforehand.

Parameters:

atomArrays - an array of Atoms for every aligned structure

Returns:

a structure object containing a set of models, one for each input array of Atoms.

Throws:

StructureException

getRMSDMatrix

public static Matrix getRMSDMatrix(MultipleAlignment msa)

Calculate the RMSD matrix of a MultipleAlignment, that is, entry (i,j) of the matrix contains the RMSD between structures i and j.

Parameters:

msa - Multiple Structure Alignment

Returns:

Matrix of RMSD with size the number of structures squared

getKimuraTree

public static org.forester.phylogeny.Phylogeny getKimuraTree(MultipleAlignment msta)
                                                      throws CompoundNotFoundException,
                                                             IOException

Calculate a phylogenetic tree of the MultipleAlignment using Kimura distances and the Neighbor Joining algorithm from forester.

Parameters:

msta - MultipleAlignment of protein structures

Returns:

Phylogeny phylogenetic tree

Throws:

CompoundNotFoundException

IOException

getHSDMTree

public static org.forester.phylogeny.Phylogeny getHSDMTree(MultipleAlignment msta)
                                                    throws CompoundNotFoundException,
                                                           IOException

Calculate a phylogenetic tree of the MultipleAlignment using dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for distantly related proteins, structure-derived) and the Neighbor Joining algorithm from forester.

Parameters:

msta - MultipleAlignment of protein structures

Returns:

Phylogeny phylogenetic tree

Throws:

CompoundNotFoundException

IOException

getStructuralTree

public static org.forester.phylogeny.Phylogeny getStructuralTree(MultipleAlignment msta)

Calculate a phylogenetic tree of the MultipleAlignment using RMSD distances and the Neighbor Joining algorithm from forester.

Parameters:

msta - MultipleAlignment of protein structures

Returns:

Phylogeny phylogenetic tree

Throws:

CompoundNotFoundException