Biology Reference
In-Depth Information
Chapter 16
PRALINE: A Versatile Multiple Sequence Alignment Toolkit
Punto Bawono and Jaap Heringa
Abstract
Profile ALIgNmEnt (PRALINE) is a versatile multiple sequence alignment toolkit. In its main alignment
protocol, PRALINE follows the global progressive alignment algorithm. It provides various alignment
optimization strategies to address the different situations that call for protein multiple sequence alignment:
global profile preprocessing, homology-extended alignment, secondary structure-guided alignment, and
transmembrane aware alignment. A number of combinations of these strategies are enabled as well.
PRALINE is accessible via the online server
http://www.ibi.vu.nl/programs/PRALINEwww/
.
The
server facilitates extensive visualization possibilities aiding the interpretation of alignments generated,
which can be written out in pdf format for publication purposes. PRALINE also allows the sequences in
the alignment to be represented in a dendrogram to show their mutual relationships according to the
alignment. The chapter ends with a discussion of various issues occurring in multiple sequence alignment.
Key words
Multiple sequence alignment, Progressive alignment, Sequence preprocessing, Homology-
extended MSA, Secondary structure-guided MSA, Transmembrane-aware protein alignment
1
Introduction
Multiple sequence alignments (MSAs) are pervasive in biology.
They are often used to elucidate conserved and variable regions in
protein or DNA sequences, which can reveal crucial information
regarding the functional and evolutionary relationships between
the aligned sequences. One of the initial breakthroughs in the
field of MSA, which addressed the computational burden asso-
ciated with MSA, was the invention of the progressive alignment
strategy [
1
].This strategy builds up an MSA by first constructing an
approximate phylogenetic tree (
guide tree
) for the query sequences
[
1
,
2
]. In many methods the guide tree is constructed from the
scores of all-against-all pairwise alignments of the query proteins.
The sequences are then progressively aligned according to the order
specified by the tree. However, an MSA produced using this
method might contain errors due to the so-called greediness of
this algorithm; i.e., alignments affected are not reconsidered any-
more and any match error occurring in the process will be
