Project Details

Bioinformatická a experimentální identifikace nekanonických struktur v genomové DNA

Project Period: 1. 4. 2008 – 31. 12. 2010

Project Type: grant

Code: GA204/08/1560

Agency: Czech Science Foundation

Program: Standardní projekty

English title
In vitro and in silico identification of non-canonical DNA structures in genomic sequences
Type
grant
Keywords

non-canonical DNA structure, palindrome, repeat, duplex, triplex, cruciform DNA, approximate pattern search, bioinformatics, FPGA

Abstract

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.

Team members
Fučík Otto, doc. Dr. Ing. (DCSY) – research leader
Burgetová Ivana, Ing., Ph.D. (DIFS)
Martínek Tomáš, doc. Ing., Ph.D. (DCSY)
Publications

2011

  • LEXA, M.; MARTÍNEK, T.; BURGETOVÁ, I.; KOPEČEK, D.; BRÁZDOVÁ, M. A dynamic programming algorithm for identification of triplex-forming sequences. BIOINFORMATICS, 2011, vol. 27, no. 18, p. 2510-2517. ISSN: 1367-4803. Detail
  • MARTÍNEK, T.; LEXA, M. Architecture Model for Approximate Tandem Repeat Detection. 22nd IEEE International Conference on Application-specific Systems, Architectures and Processors. Santa Monica, California: IEEE Computer Society, 2011. p. 239-242. ISBN: 978-1-4577-1290-6. Detail

2010

  • MARTÍNEK, T. Evaluation of Biological Sequence Similarity Using FPGA Technology. Information Sciences and Technologies Bulletin of the ACM Slovakia, 2010, vol. 2, no. 2, p. 93-102. ISSN: 1338-1237. Detail
  • MARTÍNEK, T.; LEXA, M. Hardware Acceleration of Approximate Tandem Repeat Detection. IEEE Symposium on Field-Programmable Custom Computing Machines. Charlotte: IEEE Computer Society, 2010. p. 79-86. ISBN: 978-0-7695-4056-6. Detail

2009

  • MARTÍNEK, T.; LEXA, M.; VOŽENÍLEK, J. Architecture model for approximate palindrome detection. In 2009 IEEE Symposium on Design and Diagnostics of Electronic Circuits and Systems. Liberec: IEEE Computer Society, 2009. p. 90-95. ISBN: 978-1-4244-3339-1. Detail

2008

  • MARTÍNEK, T.; LEXA, M. Hardware Acceleration of Approximate Palindromes Searching. In The International Conference on Field-Programmable Technology. Taipei: IEEE Computer Society, 2008. p. 65-72. ISBN: 978-1-4244-2796-3. Detail
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