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Odjel za računarstvo
Hrvatska sekcija IEEE, Odjel za računarstvo Hrvatske sekcije IEEE i
Zavod za primijenjeno računarstvo Fakulteta elektrotehnike i računarstva
pozivaju Vas na predavanje
"Alignment-free Estimation of Nucleotide Diversity"
koje će održati prof. Bernhard Haubold, Max Planck Institute for Evolutionary Biology, Ploen, Germany
u četvrtak, 7. listopada 2010. u 10 sati u Sivoj vijećnici FER-a.
Sadržaj predavanja i životopis predavača pročitajte u nastavku obavijesti.
Sadržaj predavanja
The cost of DNA sequencing is currently decreasing more rapidly than the cost of transistors. This
leads to a bottleneck in the computational analysis of genome sequencing data. The bulk of such analyses are based on sequence alignments. However, alignment-free sequence analysis methods tend to be more efficient than their alignment-based counterparts. They may therefore be important in the long run for keeping sequence analysis abreast with sequencing.
We derive and implement a highly efficient alignment-free estimator of the number of mismatches
between two genomes, b¼m. Our implementation of b¼m is based on an enhanced suffix array and inherits the time and memory efficiency of this data structure. Simulations demonstrate that b¼m is accurate if mutations are distributed randomly along the genome. While real data often deviate from this ideal, b¼m remains useful for sliding window analyses of local genetic diversity. We demonstrate this by applying it to the complete genomes of 37 strains of Drosophila melanogaster, and to the genomes of two closely related Drosophila species, D. simulans and D. sechellia. In both cases we detect the genome-wide diversity minimum and discuss its biological implications.
Životopis
Professor Bernhard Haubold currently leads the Bioinformatics group at the Max-Planck-Institute for Evolutionary Biology in Plön, Germany. He studied natural sciences at Cambridge University from 1988 to 1991, and German and English Language and Literature at Freiburg University from 1991 to 1994. He obtained his DPhil degree in population genetics from the Oxford University in 1998. After his doctorate, he was affiliated with the Max-Planck-Institute for Chemical Ecology in Jena from 1998 to 2001. From 2001 to 2002 he was employed as a bioinformatician at LION Bioscience AG in Heidelberg. He became a Professor of Bioinformatics at the University for Applied Sciences in Weihenstephan in 2003, where he stayed until 2008. His research interests are bioinformatics and population genetics.
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