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FRESCO: flexible alignment with rectangle scoring schemes.

A V Dalca¹, M Brudno

¹Department of Computer Science, University of Toronto, Toronto, Canada. dalcaadr@cs.toronto.edu

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

|January 31, 2008

Summary

This study introduces rectangle scoring schemes for DNA sequence alignment, enabling alignment with novel scoring functions. A new tool, FRESCO, optimizes these schemes efficiently, rivaling existing aligners.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Traditional DNA sequence alignment tools often rely on the Needleman-Wunsch scoring scheme.
Developing new scoring schemes is challenging due to the difficulty in creating optimizing algorithms.

Purpose of the Study:

To define a broad class of rectangle scoring schemes for DNA sequence alignment.
To present an algorithm and tool (FRESCO) capable of aligning sequences using arbitrary rectangle scoring schemes.
To introduce and evaluate a novel scoring function minimizing expected random diagonals.

Main Methods:

Definition of the rectangle scoring scheme class.
Development of a polynomial-time algorithm for alignment with these schemes.
Implementation of the FRESCO program for practical application.
Evaluation of a novel scoring function against established aligners.

Main Results:

The FRESCO program can align DNA sequences using any rectangle scoring scheme in polynomial time.
A novel scoring function, based on minimizing random diagonals, demonstrates performance comparable to LAGAN and Clustal-W.
The developed method does not require biological or evolutionary parameters.

Conclusions:

Rectangle scoring schemes offer a flexible framework for DNA sequence alignment.
The FRESCO tool facilitates the exploration and comparison of diverse scoring functions.
This approach provides a powerful alternative for sequence alignment without relying on traditional biological parameters.