Matthias Kruspe, Department of Computer Science, Bioinformatics Group, Leipzig University

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Overview

aln3nn is a progressive alignment tool that computes approximal exact solutions of the multiple alignment problem by the subsequent examination of sequence triplets. It is therefore predestinated to calculate more reliable alignments compared to the pairwise progressive sequence alignments approach. The alignment order is determined by means of a phylognetic network that is constructed using the NeighborNet package. To limit processor and memory usage we apply a standard divide-&-conquer approach.

The aln3nn software tool is designated to align both nucleic acid and amino acid sequences. If RNA sequences are aligned the tool provides a special feature that is to use additional structural information. This makes sense because many ncRNA evolve very quickly which means that sequence information is not always reliable. Structure in contrast evolves slowly and is therefore more stable.

Publication

Kruspe, M., Stadler, P.F. (2006) Progressive sequence alignments from Triplets, submitted
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Documentation

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Content	Type	Version	Link	Remarks
aln3nn	Source tarball	V0.34	aln3nn-0-6.0.tar.gz	latest beta

References

Bryant, D. & Moulton, V. (2002). NeighborNet: An agglomerative method for the construction of planar phylogenetic networks. In WABI '02: Proceedings of the Second International Workshop on Algorithms in Bioinformatics. Springer-Verlag, London, UK, 375-391.
Hofacker, I., Fekete, M. & Stadler, P. (2002). Secondary structure prediction for aligned RNA sequences. J. Mol. Evol., 319, 1059-1066.
Hofacker, I., Fontana, W., Stadler, P., Bonhoeffer, L., Tacker, M. & Schuster, P. (1994). Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie, 125, 167-188.
Stoye, J. (1997). Multiple sequence alignment with the divide-and-conquer method. Gene Combis, 211, 45-56.

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