Aleksandra Swiercz

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DNA sequencing by hybridization (SBH) induces errors in the biochemical experiment. Some of them are random and disappear when the experiment is repeated. Others are systematic, involving repetitions in the probes of the target sequence. A good method for solving SBH problems must deal with both types of errors. In this work we propose a new hybrid genetic(More)
Small non-coding RNAs (sncRNAs) are indispensable for proper germ cell development, emphasizing the need for greater elucidation of the mechanisms of germline development and regulation of this process by sncRNAs. We used deep sequencing to characterize three families of small non-coding RNAs (piRNAs, miRNAs, and tRFs) present in Sus scrofa gonads and(More)
In this paper, a problem of isothermic DNA sequencing by hybridization (SBH) is considered. In isothermic SBH a new type of oligonucleotide libraries is used. The library consists of oligonucleotides of different lengths depending on an oligonucleotide content. It is assumed that every oligonucleotide in such a library has an equal melting temperature. Each(More)
Recently, 454 Life Sciences Corporation proposed a new biochemical approach to DNA sequencing (the 454 sequencing). It is based on the pyrosequencing protocol. The 454 sequencing aims to give reliable output at a low cost and in a short time. The produced sequences are shorter than reads produced by classical methods. Our paper proposes a new DNA assembly(More)
DNA assembly problem is well known for its high complexity both on biological and computational levels. Traditional laboratory approach to the problem, which involves DNA sequencing by hybridization or by gel electrophoresis, entails a lot of errors coming from experimental and algorithmic stages. DNA sequences constituting the traditional assembly input(More)
In this work, a problem of DNA sequencing by hybridization (SBH) with isothermic libraries, is considered. The classical approach to SBH uses sets of oligonucleotides of equal lengths [1, 2, 8, 10, 6, 9, 7]. In isothermic SBH approach new sets of oligonucleotides are used. The library cosists of oligonucleotides with the same melting temperature but(More)