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Match

Class Match - Structure data type to hold peptide/peptide matches

Calling Sequence Match(Offset1,Offset2)
Match(Sim,Offset1,Offset2)
Match(Sim,Offset1,Offset2,Length1,Length2)
Match(Sim,Offset1,Offset2,Length1,Length2,pam)
Match(Sim,Offset1,Offset2,Length1,Length2,PamNumber,PamVariance)

Parameters

Name	Type	Description

`Sim`	numeric	similarity score of the Match
`Offset1`	posint	offset of the first sequence in the database
`Offset2`	posint	offset of the second sequence in the database
`Length1`	posint	length of the match of the first sequence
`Length2`	posint	length of the match of the second sequence
`PamNumber`	numeric	Estimate of the PAM distance between the sequences
`PamVariance`	numeric	Estimate of the PAM variance between the sequences

Return Type Match

Methods AC, Alignment, Entry, ID, print, Sequence

Synopsis The Match structure holds all the necessary information for the alignment of two peptide sequences. The offsets are positions into a peptide database, hence Match requires that an appropriate database has been loaded. The offsets are relative to the system variable DB. Typically, Match structures are initialized by giving only the two offsets. The remaining fields are completed by one of several alignment algorithms.

Examples

> DB := ReadDb('/home/darwin/DB/SwissProt.Z'):;

Peptide file(/home/darwin/DB/SP45.0/SwissProt45.0(169638448), 163235
 entries, 59631787 aminoacids)

> m:=Match( Sequence(Entry(1)), Sequence(Entry(2)) );

m := Match(376,1836)

> m2 := Match( GetOffset('UTTUWPC'), Sequence(Entry(20)));

m2 := Match(446898240,19068)

See also GetOffset, MAlign, NucPepMatch, ReadDb, TotalAlign