Biology Reference
In-Depth Information
non-existent based on the pairwise alignment process. If this option
is not specified, the default value is 1.0 (i.e., 100 %).
Option -w <value>
: Specify the number of columns in the gap-
adjustment window. Regarding the process discussed in the (-t)
option, when a column in the initial MSA is found to have at least
the necessary number of gaps to be adjusted, this value determines
the number of neighboring columns on either side to be scanned
for gaps that may be shifted into the current column. Another way
to disable this blind shifting is setting this value to 0. If this option is
not specified, the default value is 0.
The next three command-line options are available, but only useful
with the secondary-structure output from IVS, a secondary struc-
ture grammar inference program not currently released. So, it is
recommended to ignore these parameters.
3.9 Secondary
Structure Options
(Experimental)
Option -p <filename>
: Specify the grammar piece file, which is
output by IVS. By default, there is no grammar piece file used.
A grammar piece file is meant to help guide an alignment based on
secondary structure present in DNA/RNA sequences. This option
is ignored for amino acid sequences.
Option -c <value>
: Specify the grammar piece mismatch cost. This
is the subtractive penalty applied when either a residue position
being aligned is not within a structural piece but the ensemble is,
or a residue position is within a structural piece but the ensemble is
not. This amount is subtracted from the regular pairwise substitu-
tion cost. If this option is not specified, the default cost is 0.0.
Option -s <value>
: Specify the grammar piece match score. This is
the additive benefit applied when both a residue position being
aligned is contained within a structural piece and the ensemble
location is also within a structural piece. This amount is added to
the regular pairwise substitution score. If this option is not speci-
fied, the default score is 0.0.
4 Conclusion
This chapter presented
GRAMALIGN
, a computationally efficient pro-
gressive alignment method. The most interesting and novel aspects
of the algorithm involve the generation of the distance matrix
which guides the order of alignment. However, for many readers,
perhaps the most practical and useful information was presented in
Subheading
3
. That is, an in-depth detailing of the various options
that may be adjusted in order to modify the behavior and compu-
tation time necessary to complete an alignment procedure.
gramalign.php
for both source code download and a web-based
alignment server, as shown in Fig.
8
.
