Biology Reference
In-Depth Information
Fig. 7 PRALINE user-defined amino acid color table
color scheme table (Fig.
7
). Finally, PRALINE includes the option
to generate a tree based upon the MSA. However, the user should
note that trees generated by PRALINE are not phylogenetic trees,
but simply show the relationships between the sequences as deter-
mined by the alignment scores (Fig.
8
).
The following output (Figs.
6
,
8
, and
9
) is taken from an
alignment of 14 proteins belonging to the MscL family of large-
conductance mechanosensitive channels compiled together in the
BaliBASE 3.0 benchmarking database [
47
]. The alignment was
performed using the homology-extended strategy with both
integrated transmembrane and secondary structure information
from the predictions of PHOBIUS and PSIPRED, respectively.
The alignment shown in Fig.
9
is colored using the “Residue
Type” coloring scheme. The alignment shows conserved elements
as well as regions with extensive gaps. The associated tree (Fig.
8
)
clearly shows that the
1msla
sequence (bottom sequence in the
alignment) is an outlier, missing elements at both the N- and C-
termini.
