multiple sequence alignment of genomes for comparative gene prediction More...

#include <genomicMSA.hh>

Public Member Functions
	GenomicMSA (RandSeqAccess *rsa_)

void	readAlignment (string alignFilename)

void	printAlignment (string outFname)

int	numAlignments ()

GeneMSA *	getNextGene ()

void	compactify ()

void	findGeneRanges ()

void	writeDot (AlignmentGraph const &g, string fname, MsaSignature const *superSig=NULL)

void	project (AlignmentGraph &g, const MsaSignature *sig)

AliPath	getBestConsensus (AlignmentGraph &g, const MsaSignature *sig, int &numNewCovered)

int	findBestPath (AlignmentGraph &g)

bool	prunePaths (vector< AliPath > &allPaths, AlignmentGraph &g)

template<class Iterator >
bool	prunePathWrt2Other (AliPath &p, Iterator pstart, Iterator pend, AliPath &other, Iterator ostart, Iterator oend, AlignmentGraph &g, bool forward)

bool	deletePathWrt2Other (AliPath &p, AliPath &other, AlignmentGraph &g)

Static Public Member Functions
static int	weight (const Alignment a, const MsaSignature sig)

static int	weight (const Alignment a, const Alignment b, const MsaSignature *sig)

Public Attributes
vector< map< string, int > >	chrLen

Detailed Description

multiple sequence alignment of genomes for comparative gene prediction

Author: Mario Stanke

Member Function Documentation

◆ compactify()

void GenomicMSA::compactify ( )

merges pairs of alignments in order to reduce the alignment number in trivial cases without doing any potentially false mergers

Merges pairs of alignments in trivial cases in order to reduce the alignment number without doing any potentially false mergers. The priority is on avoiding mergers, where there is more than one possibility to merge. Not all trivial mergers are guaranteed to be realized, though. Trivial mergers are found by sorting with respect to a number of (unsystematically chosen) different species.

◆ findGeneRanges()

void GenomicMSA::findGeneRanges ( )

changes alignment list, so that afterwards, each alignment contains a gene range: a single alignment that may contain one or more gene, usually the merger of many .maf alignments

◆ prunePaths()

bool GenomicMSA::prunePaths	(	vector< AliPath > &	allPaths,
		AlignmentGraph &	g
	)

make several small paths from a large one that exceeds maxDNAPieceSize in one species sequence range cut off redundand ends of path and remove paths with little extra information

◆ writeDot()

void GenomicMSA::writeDot	(	AlignmentGraph const &	g,
		string	fname,
		MsaSignature const *	superSig = `NULL`
	)

write graph of all alignments into a file so graphviz can generate a picture from it

Member Data Documentation

◆ chrLen

vector<map<string,int> > GenomicMSA::chrLen

chromosome lengths as specified in the maf file for each species on hash with sequence names as keys and lengths as values

The documentation for this class was generated from the following files:

include/genomicMSA.hh
src/genomicMSA.cc

Public Member Functions

Static Public Member Functions

Public Attributes