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NucPepMatch

Class NucPepMatch

Calling Sequence NucPepMatch(NucEntries,PepEntries)
NucPepMatch(NucOffset,PepOffset)
NucPepMatch(Sim,NucOffset,PepOffset,NucLen,PepLen)
NucPepMatch(Sim,NucOffset,PepOffset,NucLen,PepLen,PamNumber)
NucPepMatch(Sim,NucOffset,PepOffset,NucLen,PepLen,PamNumber,PamVariance)
NucPepMatch(Sim,NucOffset,PepOffset,NucLen,PepLen,PamNumber,PamVariance,IntronScoring)
NucPepMatch(Sim,NucOffset,PepOffset,NucLen,PepLen,PamNumber,PamVariance,IntronScoring,NucGaps,PepGaps,Introns)

Parameters

Name	Type	Description

`Sim`	numeric	Similarity score
`NucOffset`	integer	Offset of the nucleotide sequence in NucDB
`PepOffset`	integer	Offset of the peptide sequence in PepDB
`NucLength`	integer	Length of the nucleotide sequence
`PepLength`	integer	Length of the peptide sequence
`PamNumber`	numeric	Estimated PAM distance for the match
`PamVariance`	numeric	Estimated PAM variance for the match
`IntronScoring`	{0,string,structure}	Function for scoring introns
`NucGaps`	list	Gaps in the nucleotide sequence from the alignment
`PepGaps`	list	Gaps in the peptide sequence from the alignment
`Introns`	list	List of suspected introns

Return Type NULL

Globals DB,

Methods Entry, Gene, ID, print, select, type

Synopsis The NucPepMatch structure holds all the necessary information for the alignment of a peptide and a nucleotide sequence. The offsets are positions into a peptide and nucleotide database, hence NucPepMatch requires that appropriate databases have been loaded.

Examples

See also AlignNucPepAll, AlignNucPepMatch, Denormalize, DynProgNucPepString, FindNucPepPam, Gene, GetAllNucPepMatches, GetIntrons, GetPeptides, GetPosition, GlobalNucPepAlign, Intron, LocalNucPepAlign, LocalNucPepAlignBestPam, Match, Normalize, NucDB, NucPepBackDynProg, NucPepDynProg, NucPepRegions, ParallelAllNucPepMatches, PepDB, ScoreIntron, VisualizeGene, VisualizeProtein