Engineering: Evolutionary software for free

New science-aiding software to help scientists with proteins and nucleic acids analysis has been developed by researchers at the University of Illinois (U of I).

The software allows scientists to more effectively analyse and compare both sequence and structure data from a growing library of proteins and nucleic acids.
 
"MultiSeq (pronounced Multi-seek) allows you to bring in both structure and sequences without structure, and use the complementary information contained within them to investigate changes in the system," said Zaida Luthey-Schulten, a professor of chemistry and a researcher at the Beckman Institute for Advanced Science and Technology at the U of I.
 
"By placing bioinformatics in the context of evolution, we can also perform comparative dynamics studies of proteins from different domains of life," she added.
 
The organisation of this data is a welcome addition to the science community as there are currently more than three million sequences and 35,000 structures of proteins and nucleic acids available for study.
 
By providing an environment for the evolutionary analysis of this data, the software can help scientists gain valuable insight into basic scientific questions, such as the origin of life, as well as questions of a more practical nature, such as the development of resistance to ribosome-targeting antibiotics.
 
MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of a programme for visualising and analysing molecular dynamics simulations, called Visual Molecular Dynamics (VMD).
 
A welcome aspect of the new software release is that it will be distributed free of charge.
 
VMD is designed to efficiently handle large three-dimensional systems containing more than a million atoms.

Multiseq takes biological data analysis to a new level

MultiSeq extends VMD's capabilities by incorporating the more diverse evolutionary data available in sequences into the analysis process.
 
For example, the computational tools in MultiSeq may help scientists understand the evolution of ribosomes, the basic machinery of translation.
 
Translation is a key component of all life, and the components of this cellular machinery are the biomolecules with the most linear line of descent.
 
"If we want to try and understand how translation has changed among the three domains of life, we have to at least be able to overlap and compare three ribosomes," Luthey-Schulten said.
 
"Last year, we could not compare two ribosomes. Now, using MultiSeq, we can compare more than 20 ribosomes."
 
The software is described in a paper published in the journal BMC Bioinformatics.
 
It will be used in US classrooms this autumn as a teaching tool for computational chemical biology.
 
"This approach can speed up research by revealing unproductive tasks in advance or by exposing new paths through the introduction of distant but related data," the researchers wrote.

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