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Clustal Omega: The ultimate alignment programme?

How would you compare the sequence of a histone protein across 10,000 different species? Until now the question was partly an abstract one because the technology for generating sequences was slow and expensive. 

Today, rapid advances in technology and the falling cost of genome sequencing are facilitating proposals to sequence 1000 human genomes (http://www.1000genomes.org) and 10,000 vertebrate genomes (http://www.genome10k.org).  Future scientific studies may have to compare 100,000s of sequences and databases will house millions of genome sequences.

Modern approaches to aligning very large numbers of sequences are starting to become a bottleneck when facing such large data sets. They are either fast yet generate unacceptably poor quality alignments or they are accurate yet prohibitively intensive of computing power.

UCD researchers led by Professor Des Higgins and their collaborators in Europe, Asia and the USA have addressed these issues using Clustal Omega, a new programme recently described in Molecular Systems Biology, a scientific journal produced jointly by Nature and EMBO.

Clustal Omega can align virtually any number of protein sequences quickly and delivers accurate alignments. One novel aspect is the use of vectors to reduce the complexity of a key step in the algorithm, dramatically reducing the processing time.  Currently, the programme is designed to align protein sequences (not nucleic acids) but can run on a personal computer or over a server and is available at http://www.clustal.org.

Des Higgins developed the original Clustal programme for aligning protein sequences in 1988, which has become one of the most highly cited bioinformatics papers ever. One of the innovations of that programme was that the algorithm was designed to work on personal computers, which greatly increased its use among scientists.

This work was funded by Science Foundation Ireland.

Reference:
Fabian Sievers, Andreas Wilm, David Dineen, Toby J. Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Soding, Julie D. Thompson, Desmond G. Higgins (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.  Molecular Systems Biology, Vol. 7, No. 1. msb.2011.75.

Higgins DG, Sharp PM (1988). "CLUSTAL: a package for performing multiple sequence alignment on a microcomputer". Gene 73 (1): 237–244