Evolutionary software to be released free of charge

Sep 18, 2006

New software developed by researchers at the University of Illinois at Urbana-Champaign allows scientists to more effectively analyze 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."

Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are 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.

Developed by Luthey-Schulten and graduate students Elijah Roberts, John Eargle and Dan Wright, MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD (Visual Molecular Dynamics), a program for visualizing and analyzing molecular dynamics simulations. Developed at the U. of I. and distributed free of charge, VMD is designed to efficiently handle large three-dimensional systems containing more than a million atoms. 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."

MultiSeq combines both sequence and structure data within an evolutionary framework using information science to organize and search the data, information visualization to assist in recognizing correlations, mathematics to formulate statistical inferences, and biology to analyze chemical and physical properties in terms of sequence and structure changes.

The researchers developed MultiSeq in collaboration with the Theoretical and Computational Biophysics group at the Beckman Institute, and with the NIH (National Institutes of Health) Resource for Macromolecular Modeling and Bioinformatics. They describe the software in a paper accepted for publication in the journal BMC Bioinformatics, and featured on the journal's Web site. The software is being used in classrooms this fall as a teaching tool for computational chemical biology.

"We believe the complexity present in biology can not be fully understood without using evolution as an underlying framework," the researchers write. "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."

For details on how to download and use the software, visit the MultiSeq website at: www.scs.uiuc.edu/~schulten/multiseq/

Source: University of Illinois at Urbana-Champaign

Explore further: Liquid helium offers a fascinating new way to make charged molecules

add to favorites email to friend print save as pdf

Related Stories

MasterCard, Zwipe announce fingerprint-sensor card

5 hours ago

On Friday, MasterCard and Oslo, Norway-based Zwipe announced the launch of a contactless payment card featuring an integrated fingerprint sensor. Say goodbye to PINs. This card, they said, is the world's ...

Plastic nanoparticles also harm freshwater organisms

7 hours ago

Organisms can be negatively affected by plastic nanoparticles, not just in the seas and oceans but in freshwater bodies too. These particles slow the growth of algae, cause deformities in water fleas and impede communication ...

Atomic trigger shatters mystery of how glass deforms

7 hours ago

Throw a rock through a window made of silica glass, and the brittle, insulating oxide pane shatters. But whack a golf ball with a club made of metallic glass—a resilient conductor that looks like metal—and the glass not ...

US company sells out of Ebola toys

15 hours ago

They might look tasteless, but satisfied customers dub them cute and adorable. Ebola-themed toys have proved such a hit that one US-based company has sold out.

UN biodiversity meet commits to double funding

15 hours ago

A UN conference on preserving the earth's dwindling resources wrapped up Friday with governments making a firm commitment to double biodiversity aid to developing countries by 2015.

Recommended for you

Amino acids key to new gold leaching process

21 hours ago

Curtin University scientists have developed a gold and copper extraction process using an amino acid–hydrogen peroxide system, which could provide an environmentally friendly and cheaper alternative to ...

Researchers create designer 'barrel' proteins

Oct 23, 2014

Proteins are long linear molecules that fold up to form well-defined 3D shapes. These 3D molecular architectures are essential for biological functions such as the elasticity of skin, the digestion of food, ...

User comments : 0