. . " duplex" . . . " triplex" . . . . . "The presented project focused on combining the newest technology in the area of hardware acceleration, molecular biology and bioinformatics. The goal was to understand, predict and map the occurrence of biologically important non-canonical structures in human genomic DNA. The collaboration between the three participating institutions leads to the creation of algorithms and computational tools cap"@en . . "2010-04-16+02:00"^^ . "2010-12-31+01:00"^^ . . . . " palindrome" . . "non-canonical DNA structure; palindrome; repeat; duplex; triplex; cruciform DNA; approximate pattern"@en . . "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"@en . "17"^^ . "non-canonical DNA structure" . "In vitro and in silico identification of non-canonical DNA structures in genomic DNA sequences"@en . "17"^^ . "Bioinformatick\u00E1 a experiment\u00E1ln\u00ED identifikace nekanonick\u00FDch struktur v genomov\u00E9 DNA" . . "Sekvenov\u00E1n\u00ED genom\u016F zv\u00FD\u0161ilo z\u00E1jem nejen o nek\u00F3duj\u00EDc\u00ED DNA, ale i o nekanonick\u00E9 struktury, kter\u00E9 mohou b\u00FDt nek\u00F3duj\u00EDc\u00ED DNA vytv\u00E1\u0159eny, a jejich mo\u017En\u00E9 biologick\u00E9 funkce. V tomto n\u00E1vrhu hodl\u00E1me skloubit nejnov\u011Bj\u0161\u00EDmi technologiemi molekul\u00E1rn\u00ED biologii s bioinformatikou ve snaze pochopit, p\u0159edpov\u00EDdat a mapovat v lidsk\u00E9m genomu v\u00FDskyt biologicky d\u016Fle\u017Eit\u00FDch struktur. Na z\u00E1klad\u011B p\u0159edch\u00E1zej\u00EDc\u00EDho v\u00FDskumu se experiment\u00E1ln\u011B soust\u0159ed\u00EDme hlavn\u011B na detekci k\u0159\u00ED\u017Eov\u00FDch struktur DNA a triplex\u016F DNA. Zmodernizujeme a v p\u0159\u00EDpad\u011B k\u0159\u00ED\u017Eov\u00FDch struktur vytvo\u0159\u00EDme v\u00FDpo\u010Detn\u00ED n\u00E1stroj pro predikci t\u011Bchto struktur v genomov\u00E9 DNA. Aplikace bude zah\u00E1jena s regula\u010Dn\u00EDmi oblastmi n\u00E1dorov\u00FDch supresor\u016F a onkogen\u016F (nap\u0159. p53) \u010Di jejich c\u00EDlov\u00FDch gen\u016F (nap\u0159. EGFR, c-myc, hsp90) studovan\u00FDch vlaborato\u0159i navrhovatele. Rychlost po\u010D\u00EDta\u010Dov\u00E9ho zpracov\u00E1n\u00ED cel\u00FDch genom\u016F doc\u00EDl\u00EDme vyu\u017Eit\u00EDm vhodn\u00FDch algoritm\u016F a jejich implementaci s podporou hradlov\u00FDch pol\u00ED (FPGA). Takto budeme schopni rychle a s vy\u0161\u0161\u00ED citlivost\u00ED anotovat genomy z pohledu v\u00FDskytu" . "2015-02-09+01:00"^^ . "0"^^ . . . "2008-04-01+02:00"^^ . " repeat" . "GA204/08/1560" . "1"^^ . " cruciform DNA" . "2"^^ . "\u0158e\u0161en\u00FD projekt se zam\u011B\u0159il na sklouben\u00ED nejnov\u011Bj\u0161\u00EDch technologi\u00ED v oblasti hardwarov\u00FDch akcelerac\u00ED, molekul\u00E1rn\u00ED biologie s bioinformatikou ve snaze pochopit, p\u0159edpov\u00EDdat a mapovat v lidsk\u00E9m genomu v\u00FDskyt biologicky d\u016Fle\u017Eit\u00FDch struktur. Na z\u00E1klad\u011B spolupr\u00E1ce trojice pracovi\u0161\u0165 z t\u011Bchto oblast\u00ED bylo mo\u017En\u00E9 vytvo\u0159it algoritmy a n\u00E1stroje schopn\u00E9 vyhled\u00E1vat v DNA sekven\u010Dn\u00ED vzory zodpov\u011Bdn\u00E9"@cs . "http://www.isvav.cz/projectDetail.do?rowId=GA204/08/1560"^^ . . . .