How KalignP works
KalignP changes the behavior of the alignment intuitively with the
externally supplied position specific gap penalties. Generally
speaking, if the users want to force a gap after the first residue
of a sequence, set the gap open penalty at the second residue
position of that sequence to a small value. For example, for the
following four sequences,
>seq1
ASNLSKLFLSDSDA
>seq2
ASNLDA
>seq3
ASNLKFFFDDDAA
>seq4
LLNFFSDAAAAA
The multiple sequence alignment (MSA) with all parameters set
to default is as follows (in ClustalW format)
seq1 ASNLSKLFLSDSDA-
seq2 ASNLDA-----
seq3 ASNLKF-FFDDDAA-
seq4 LLN--FFSDAAAAA
The tree of the MSA is (((seq1, seq2), seq3), seq4). If the users want to open
a gap after the second residue in seq1, the users can set the gap open penalty
at the third position to be a minus value (e.g. -5). An example setting of
ESPSGP is as follows. To ensure that only one gap is opened after the second
residue S in seq1 so that we can see clearly the effect of gap open, we have
set the gap open penalties for seq2 and the gap open penalty at the fourth
position of seq1 to be a large positive value.
>seq1
ASNLSKLFLSDSDA
{gpo: 1 1 -5 10 1 1 1 1 1 1 1 1 1 1 }
>seq2
ASNLDA
{gpo: 10 10 10 10 10 10 }
>seq3
ASNLKFFFDDDAA
>seq4
LLNFFSDAAAAA
The alignment will become
seq1 AS-NLSKLFLSDSDA-
seq2 -ASNLDA-----
seq3 -ASNLKF-FFDDDAA-
seq4 --LLN-FFSDAAAAA
If the users want again to open a gap after the 11th residue D in seq3, set the gap open penalty of the 11th position in seq3 to a minus value (e.g. -5). An example ESPSGP setting is as follows. Again, to ensure that gap will only be opened after the 11th residue in seq3, we have set the gap open penalty of seq4 and the neighboring residue positions in seq3 to large positive values.
>seq1
ASNLSKLFLSDSDA
{gpo: 1 1 -5 10 1 1 1 1 1 1 1 1 1 1 }
>seq2
ASNLDA
{gpo: 10 10 10 10 10 10 }
>seq3
ASNLKFFFDDDAA
{gpo: 1 1 1 1 1 1 1 1 1 10 -5 20 10 }
>seq4
LLNFFSDAAAAA
{gpo: 10 10 10 10 10 10 10 10 10 10 10 10}
The alignment will become
seq1 -----AS-NLSKLFLSDSDA
seq2 -----ASNLDA----
seq3 ASNLKFFFDD--DAA----
seq4 ------LLNFFSDAAAAA
The alignment above might not be ideal since there are many gaps at the terminals. To reduce the number of terminal gaps, one can increase the terminal gap extension penalty as shown in the example below.
>seq1
ASNLSKLFLSDSDA
{gpo: 1 1 -5 10 1 1 1 1 1 1 1 1 1 1 }
{tgpe: 10 10 10 10 10 10 10 10 10 10 10 10 10 10}
>seq2
ASNLDA
{gpo: 10 10 10 10 10 10 }
{tgpe:10 10 10 10 10 10}
>seq3
ASNLKFFFDDDAA
{gpo: 1 1 1 1 1 1 1 1 1 10 -5 20 10}
{tgpe: 10 10 10 10 10 10 10 10 10 10 10 10 10}
>seq4
LLNFFSDAAAAA
{gpo: 10 10 10 10 10 10 10 10 10 10 10 10}
{tgpe:10 10 10 10 10 10 10 10 10 10 10 10}
The alignment will become
seq1 AS-NLSKLFLSDS-DA
seq2 -ASNLDA-----
seq3 AS-NLKFFFDD-D-AA
seq4 --LLNFFSDAAAAA-
Sometimes, the gap will not be opened at the expected position if many customized gap penalties are set in multiple sequences. This is because KalignP forbid neighboring gap opens at two aligned sequences such as the following example
ALDDS-D-S
ALED-D-S-
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