Biology Reference
In-Depth Information
Suggestion:
This value determines the amount of the pairwise
matrix that is calculated when aligning consensus sequences.
Thus, they are less likely to be nearly identical, and so more of the
matrix should be calculated.
3.7 Alignment
Scoring Options
GRAMALIGN
uses the following parameters for the pairwise alignment
process, which is an affine-gap version of Needleman-Wunsch.
Option -g <value>
: Specify the gap-open cost. At the core of the
alignment algorithm is the pairwise alignment algorithm used to
progressively align each sequence not already in the alignment. This
pairwise process is the well-known Needleman-Wunsch dynamic
programming algorithm modified for affine gap penalties. The
value specified in this option represents the cost assigned anytime
a gap in a sequence is started. If this option is not specified,
the default value is 15.2 for protein sequences or 8.7 for DNA
sequences. In the case the GONNET250 substitution matrix is
used, this value is multiplied by 10.
Option -G <value>
: Specify the tail gap-open cost. The value
specified in this option represents the cost assigned if a gap is started
at either the beginning or the ending of the alignment. If this
option is not specified, the default value is 15.2 for protein
sequences or 8.7 for DNA sequences. In the case the GON-
NET250 substitution matrix is used, this value is multiplied by 10.
Option -e <value>
: Specify the gap-extension cost. The value
specified in this option represents the cost assigned each time a
gap in a sequence is extended by an additional character. If this
option is not specified, the default value is 0.6 for protein sequences
or 0.8 for DNA sequences. In the case the GONNET250 substitu-
tion matrix is used, this value is multiplied by 10.
Option -E <value>
: Specify the tail gap-extension cost. The value
specified in this option represents the cost assigned each time a gap
is extended at either the beginning or the ending of the alignment.
If this option is not specified, the default value is 0.3 for protein
sequences or 0.4 for DNA sequences. In the case the GON-
NET250 substitution matrix is used, this value is multiplied by 10.
Option -m <value>
: Specify the amino acid substitution matrix.
Another important piece of the Needleman-Wunsch pairwise align-
ment procedure is the substitution scoring matrix. A value of 0 will
use the GONNET250matrix. A value of 1 will use the BLOSUM45
matrix. A value of 2 will use the BLOSUM62 matrix. A value of 3
will use the BLOSUM80 matrix. Note, when using the GON-
NET250 matrix, the values specified by -g, -G, -e, and -E are all
multiplied by 10 to account for the relative differences between the
GONNET and BLOSUM matrices. If this option is not specified,
the default substitution matrix is the GONNET250. This option is
ignored for nucleotide sequences, which use a simple matrix of
positive diagonal entries and negative off-diagonal entries.
