Doc. Dr. Ing. Otto Fučík

In vitro and in silico identification of non-canonical DNA structures in genomic sequences

Czech title:Bioinformatická a experimentální identifikace nekanonických struktur v genomové DNA
Team leaders:Fučík Otto, Martínek Tomáš, Rudolfová Ivana
Agency:Grantová agentura AV ČR
Keywords:non-canonical DNA structure, palindrome, repeat, duplex, triplex, cruciform DNA, approximate pattern search, bioinformatics, FPGA
Genomic sequencing generated an increased interest in non-coding DNA. This applies also to non-canonical DNA structures and their possible biological functions. Here we propose to combine molecular biology, bioinformatics and the latest computer technology in an effort to understand, predict and map the occurrence of biologically important DNA structures in genomes. Motivated by our previous research, we will focus on
non-canonical DNA structures (cruciforms, triplex, slippage- and Z-DNA). We will improve (and where necessary develop) tools for in silico prediction of these DNA structures. Predictions will be verified by carefully planned laboratory experiments, focusing on promoter regions of cancer-related genes (e.g. p53, MDM2, hsp90, EGFR) studied in the applicant's laboratory. Our ability to rapidly analyze full genomes will come from the use of special algorithms and applications built around FPGA hardware-acceleration cards.

As a result, we will obtain annotations of genomes for predicted structures, occurence of such structures in
oncogenes, as well as new methods and hardware for wider applications of accelerated sequence search.


2010Identification of palindrome-forming sequences, software, 2010
Authors: Martínek Tomáš, Lexa Matej
 Identification of triplex-forming sequences, software, 2010
Authors: Martínek Tomáš, Lexa Matej, Kopeček Daniel, Burgetová Ivana


2011LEXA Matej, MARTÍNEK Tomáš, BURGETOVÁ Ivana, KOPEČEK Daniel and BRÁZDOVÁ Marie. A dynamic programming algorithm for identification of triplex-forming sequences. Bioinformatics. Oxford: Oxford University Press, 2011, vol. 27, no. 18, pp. 2510-2517. ISSN 1367-4803.
 MARTÍNEK Tomáš and LEXA Matej. Architecture Model for Approximate Tandem Repeat Detection. In: 22nd IEEE International Conference on Application-specific Systems, Architectures and Processors. Santa Monica, California: IEEE Computer Society, 2011, pp. 239-242. ISBN 978-1-4577-1290-6.
2010MARTÍNEK Tomáš and LEXA Matej. Hardware Acceleration of Approximate Tandem Repeat Detection. In: IEEE Symposium on Field-Programmable Custom Computing Machines. Charlotte: IEEE Computer Society, 2010, pp. 79-86. ISBN 978-0-7695-4056-6.
 MARTÍNEK Tomáš. Evaluation of Biological Sequence Similarity Using FPGA Technology. Information Sciences and Technologies Bulletin of the ACM Slovakia. Bratislava: Vydavateľstvo STU, 2010, vol. 2, no. 2, pp. 93-102. ISSN 1338-1237.
2009MARTÍNEK Tomáš, LEXA Matej and VOŽENÍLEK Jan. Architecture model for approximate palindrome detection. In: 2009 IEEE Symposium on Design and Diagnostics of Electronic Circuits and Systems. Liberec: IEEE Computer Society, 2009, pp. 90-95. ISBN 978-1-4244-3339-1.
2008MARTÍNEK Tomáš and LEXA Matej. Hardware Acceleration of Approximate Palindromes Searching. In: The International Conference on Field-Programmable Technology. Taipei: IEEE Computer Society, 2008, pp. 65-72. ISBN 978-1-4244-2796-3.

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