Biology Reference
In-Depth Information
Fig. 2 Schematic overview of the homology-extended alignment strategy. For
details, see text. Adapted from ref.
18
alignments for each sequence are converted to a pre-profile and
then become progressively aligned using the core MSA method
described in Subheading
1
(Fig.
2
).
The main advantage of this approach is that it uses a much
greater amount of position-specific information in the profile scor-
ing scheme due to the homology-extended profiles based upon
potentially large numbers of putatively homologous sequences.
This greatly helps the alignment of sequences, particularly those
in the twilight zone (
<
30 % sequence identity) or even in more
divergent cases [
18
].
In addition to global profile preprocessing, PRALINE also
incorporates local profile preprocessing. However, since this imple-
mentation is essentially equivalent to the homology-extended strat-
egy based upon PSI-BLAST searches described here, but is less
successful in general due to the inclusion of input sequences only,
it is not enabled as an option in the PRALINE Web server.
