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: Computational clues into the structure of a promising energy conversion catalyst

add to favorites email to friend print save as pdf

Related Stories

Microbial 'signature' for sexual crimes

5 hours ago

Bacterial communities living on an individual's pubic hairs could be used as a microbial 'signature' to trace their involvement in sexual assault cases, according to a study published in the open access journal Investigative Ge ...

Brazil: Google fined in Petrobras probe

7 hours ago

A Brazilian court says it has fined Google around $200,000 for refusing to intercept emails needed in a corruption investigation at state-run oil company Petrobras.

Atari's 'E.T.' game joins Smithsonian collection

7 hours ago

One of the "E.T." Atari game cartridges unearthed this year from a heap of garbage buried deep in the New Mexico desert has been added to the video game history collection at the Smithsonian.

Sony threatens to sue for publishing stolen emails

7 hours ago

A lawyer representing Sony Pictures Entertainment is warning news organizations not to publish details of company files leaked by hackers in one of the largest digital breaches ever against an American company.

Microsoft builds support over Ireland email case

7 hours ago

Microsoft said Monday it had secured broad support from a coalition of influential technology and media firms as it seeks to challenge a US ruling ordering it to hand over emails stored on a server in Ireland.

Recommended for you

A renewable bioplastic made from squid proteins

8 hours ago

In the central Northern Pacific is an area that may be the size of Texas called the Great Pacific Garbage Patch. Made up of tons of floating plastic debris, the patch is killing seabirds and poisoning marine ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.