Abstract:
The mandatory first step for a wide range of biological analyses is the alignment of short DNA sequences into a reference genome. We first discuss a method, extending Rabin and Karp's algorithm, to find all occurrences of a pattern P with up to k mismatches inside a text T, with average complexity O(|P| + |T|)--assuming an uniform distribution over T. We then show how to employ this idea in conjunction with an index over T, allowing to search P with mismatches in time proportional to its length. Our novel tool--rNA (randomized Numerical Aligner)--is in general faster and more accurate than other widely used tools like SOAP2, BWA, and BOWTIE.
Joint work with C. Del Fabbro, A. Policriti, F. Vezzi
Biography:
Alexandru Tomescu, graduate of the University of Bucharest (Romania), recently obtained his PhD in Computer Science from the University of Udine (Italy); he is currently visiting the TU Berlin (Germany). Alexandru's PhD thesis focuses on graphs and sets with the goal of a transfer of structural and algorithmic notions and results across the two areas. He also collaborated with the bioinformatics group at the Institute of Applied Genomics in Udine on designing a method to rapidly and accurately map (short) DNA sequences into reference genomes.