Book of Abstracts Program Committee

Polish Bioinformatics Society Institute of Computing Science, Poznań University of Technology Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań II Convention of the Polish Bioinformatics Society in conjunction with 7th Workshop on Bioinformatics Będlewo, October 2–4, 2009 Book of Abstracts Program Committee Jacek Błażewicz (Chair) Institute of Computing Science, Poznań University of Technology, Poznań, Poland Jerzy Tiuryn Institute of Informatics, University of Warsaw, Warsaw, Poland Wiesław Nowak Institute of Physics, Nicolaus Copernicus University, Toruń, Poland Janusz M. Bujnicki Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland Organizing Committee Marta Kasprzak (Chair) Marta Szachniuk Marcin Borowski Institute of Computing Science, Poznań University of Technology, Poznań, Poland 2 Workshop Overview The following Book of Abstracts contains the talks to be presented at the 7th Workshop on Bio- informatics, to be held in Będlewo, October 2–4, 2009. The first five workshops gathered mostly Ph.D. students and senior researchers from two centers — University of Warsaw (Institute of In- formatics) and Poznań University of Technology (Institute of Computing Science). Since the last year the workshop is organized in a conjuction with the Convention of the Polish Bioinformatics Society and has a much wider representation of the centers and topics to be discussed. This year, due to the vast outcome of the call for presentations and the technical constraints imposed on the organizers, not all of the submitted talks could be accepted. The Program Committee after a thorough refereeing procedure included into the final program 29 talks. The accepted talks are concerned with several topics dominating current bioinformatics and computational biology areas. Most of them (10 talks) deal with different models of protein structure analysis and prediction. Second biggest area is the RNA structure analysis and modeling (4 talks). Analysis of DNA sequences (assembly algorithms and motif discovery) and improve- ment of alignment algorithms as well as evolution issues are the topics of 3 talks each. Other topics discussed are: gene clusters (2 talks), disease and immunology issues (2 talks) and finally signaling pathways and text mining (1 talk each). All the talks discuss problems of a very high importance and the level of the results obtained is very good. Speakers represent different bioinformatics centers in Poland, in particular: Adam Mickiewicz University (Bioinformatics Laboratory at Institute of Molecular Biology and Biotechnology), Poznań — 9 talks; University of Warsaw (Institute of Informatics and Interdisciplinary Centre for Mathematical and Computational Modelling) — 8 talks, Poznań University of Technology (Institute of Computing Science) — 7 talks, Nencki Institute of Experimental Biology, Warsaw — 2 talks, Silesian University of Technology, Gliwice (Institute of Informatics) — 2 talks, and finally International Institute of Molecular and Cell Biology (Laboratory of Bioinformatics and Protein Engineering), Warsaw — 1 talk. Here, I would like to thank all the members of Program and Organizing Committees for their help in evaluating talks and organizing the meeting. Special thanks are due to Marta Kasprzak who, as the Chair of the Organizing Committee, gave the right momentum to the work of these two bodies, devoting a lot of her energy and skills to the success of our workshop. Prof. Jacek Błażewicz Chair of the Program Committee 3 Contents Michał Startek, Anna Gambin, “Evolving subset seeds for finding protein alignment” . 6 Łukasz Ligowski, Witold Rudnicki, “Comparison of PSI-BLAST and PSI-Smith-Waterman algorithms” ....................................... 6 Paweł Wojciechowski, “Parallel implementation of T-COFFEE algorithmonGPU” .. 7 Piotr Gawron, “Parallel algorithm for DNA assembly” . ...... 7 Tomasz Głowacki, Marcin Borowski, Piotr Formanowicz, “Long peptides assembly me- thodbasedonEdmandegradation” . .. 8 Rafał Pokrzywa, “Searching for tandem repeats in DNA sequences using the Burrows- Wheelertransform”................................... 9 Miron Kursa, “WAIAS — a web toolkit for an aptamer analysis” . ..... 9 Sławomir Walkowiak, Konrad Wawruch, Łukasz Ligowski, Witold Rudnicki, “Searching biochemicalcompoundsintextdatabases” . .... 10 Aleksandra Gruca, “Gene ontology based characterization of groups of genes by multi- attributerules” ..................................... 11 Dariusz Plewczyński, “Virtual high-throughput screening using machine learning & do- cking” .......................................... 11 Teresa Szczepińska, Krzysztof Pawłowski, “Looking for chromosome spatial organization rulesinmicroarraygeneexpressiondata” . ... 12 Ewa Szczurek, Florian Markowetz, Irit Gat-Viks, Przemysław Biecek, Jerzy Tiuryn, “Model-based dissection of transcriptional deregulation” . ........ 13 Marcin Jąkalski, Izabela Makałowska, “Evolution of overlapping genes in Drosophila genomes” ........................................ 14 Aleksander Jankowski, “Predicting nucleosome binding sites in yeast genome” . 15 Mikołaj Rybiński, Anna Gambin, Haluk Resat, “Testing for heterogenity in the recep- torsdensity”....................................... 15 Joanna Ciomborowska, Damian Szklarczyk, Wojciech Makałowski, Izabela Makałowska, “Retrogenes: the genesis and evolutionary consequences” . .......... 16 Michał Szcześniak, Michał Kabza, Joanna Ciomborowska, Izabela Makałowska, “Intron gaininmammals” ................................... 17 Szymon Wąsik, “On a certain model of HCV infection” . ..... 17 Małgorzata Maciukiewicz, “Association analysis in human diseases: schizophrenia and bipolar affective disease example” . 18 Wojciech Karłowski, Andrzej Zieleziński, “Computational identification and comparative analysis of ARGONAUTE-binding platforms found in plant RRM proteins” . 19 Anna Lenart, Krzysztof Pawłowski, “Comparative modeling of the hydrolase domain fromdifferentCLCAproteins” ............................ 19 Arkadiusz Hoffa, Piotr Łukasiak, Maciej Antczak, Jacek Błażewicz, “Ligand-protein conformationstructureprediction” . .... 20 Maciej Antczak, Piotr Łukasiak, Maciej Miłostan, Jacek Błażewicz, “DomAn2 – approach for predicting domains boundaries in proteins” . .... 21 Wojciech Potrzebowski, Janusz M. Bujnicki, “A novel method for tracing polypeptide chains in medium-resolution electron density maps” . .... 22 Joanna M. Kasprzak, Wojciech Potrzebowski, Janusz M. Bujnicki, Kristian Rother, “Modeling of large macromolecular complexes” . ... 22 4 Agnieszka Rybarczyk, “Branch and cut algorithm for the RNA degradation problem” . 23 Anna Philips, “Prediction of metal-binding sites in RNA structures” . ........ 23 Magdalena Musielak, Kristian Rother, Tomasz Puton, Janusz M. Bujnicki, “RNA ter- tiarystructurepredictionwithModeRNA” . ... 24 Tomasz Puton, Kristian Rother, Janusz M. Bujnicki, “CompaRNA — a server for comparison of methods for RNA structure prediction” . ...... 24 5 Evolving subset seeds for finding protein alignment Michał Startek a∗, Anna Gambin a (a) Institute of Informatics, University of Warsaw, Warsaw, Poland (∗) [email protected] Abstract During this talk, a modification of BLAST algorithm will be presented. The modification is based on replacing the standard substitution table used by BLAST (like BLOSUM) with a so-called subset seed (chosen specifically for the protein family being aligned), that represents structural information about the family. Using such a seed, it becomes possible to find structurally signifi- cant alignments from the so-called ‘twilight zone’ of BLAST algorithm, namely alignments with low identity percentage, that anyway represent a conserved domain. Choosing a proper subset of seeds for particular protein family, however, poses an interesting computational problem. We will present a solution for this problem using an evolution algorithm. Comparison of PSI-BLAST and PSI-Smith-Waterman algorithms Łukasz Ligowski a∗, Witold Rudnicki a (a) Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland (∗) [email protected] Abstract PSI-BLAST is basic tool to detect distant evolutionary relationships between proteins. It uses BLAST for scanning protein database for similar sequences. BLAST heuristics scans databases very fast while retaining good levels of specificity and sensitivity. However plain BLAST does not provide quality results like precise methods such as Smith-Waterman algorithm. Until now, employment of Smith-Waterman algorithm for large database scans was unfeasi- ble due to prohibitive computation time. Several high performance implementations of Smith- Waterman algorithm emerged on different hardware architectures. In order to create PSI-SW we used our previous work, which is Smith-Waterman on NVIDIA CUDA. Our implementation matches BLAST speed but Smith-Waterman algorithm produces significantly better results than BLAST. Our main interest is to find out if using PSI-* approach benefits from using different search engine that produces better results. We hope that using better engine will produce significantly better results in first and subsequent iterations. Our presentation will contain discussion of PSI-SW and PSI-BLAST results on SCOP database. Comparing two search engines by using only ROC curves calculated in straightforward way can produce misleading results depending on reference database composition. We will present detailed analysis of results

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