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GetOffset

Calling Sequences:
GetOffset(
seq)
Parameters:
seq : string

Returns: integer

Synposis: The GetOffset places seq into the sequence database assigned to DB. All string objects must be given an offset from DB before any alignment algorithm GlobalAlign, LocalAlignBestPam, etc. can be applied to them.

The GetOffset requires that the system variable DB must be assigned a sequence database.

Examples:

> DB := ReadDb('~cbrg/DB/SwissProt'):   CreateDayMatrices():
> s1 := 'MSRYEKMFARLNERNQGAFVPFVTVCDPNAEQSYKIMETLVESGADALELGIPFSDP':
> s2 := 'MLLLSVNPPLFIPFIVAGDPSPEVTVDLALALEEAGADLLELGVPYSDP':
> m3 := Match( GetOffset(s1), GetOffset(s2) );
> print(LocalAlignBestPam(m3, DMS));




Gaston Gonnet
1998-09-15