Bioinformatická a experimentální identifikace nekanonických struktur v geonomové DNA
Project Period: 1. 4. 2008 - 31. 12. 2010
Project Type: grant
Agency: Grantová agentura AV ČR
Program: Standardní projekty
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.