The Match Structure

The routines DynProg and BackDynProg are low-level commands operating directly on string objects. The alignment routines through the remaining part of this chapter require an offset into a Darwin database be given for the sequences. The routines available for accessing information contained in the Darwin sequence databases are explained in Chapter  - Genetic Databases.

The structured type Match holds a partial or totally defined alignment between two amino acid sequences. A match can have as little information as two offsets, for example:

> DB:=ReadDb('Sample/SH2'):
> m1 := Match(367, 1338);          # offset for sequence #1 and #2.
m1 := Match(367,1338)

Offset 367 from DB[string] marks the beginning of the sequence in the first entry of the SH2 database. Offset 1338 is the beginning of the sequence for the second entry (see page ). Instead of giving the offset directly to Match, we could have used the Sequence and Entry structures to find these offsets for us.

> m1 := Match(op(Sequence(Entry(1))), op(Sequence(Entry(2))));
m1 := Match(367,1338)
> m1[Offset1];                  # offset of first sequence
367
> m1[Offset2];                  # offset of second sequence
1338
> Entry(m1);
Entry(1,2)
> Offset(m1);
Offset(367,1338)

Table  gives a complete list of the selectors available for this type.

Table: Selectors for the Match structured type.

1.1 

Table: Selectors for the Match structured type.

Selector	Description
Sim	Similarity score of the match
Offset1	Offset of the first sequence in the database
Offset2	Offset of the second sequence in the database
Length1	Length of the match of the first sequence
Length2	Length of the match of the second sequence
PamNumber	estimate of the PAM distance between the sequences
PamVariance	estimate of the PAM variance between the sequences