TR Dizin İndeksli Yayınlar Koleksiyonu / TR Dizin Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14365/4
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Article A Comparative study of DNA Alignment Algorithms and Boosting Performance Using Different Compilation Strategies(2024-12-30) Doluca, OsmanYeni nesil sekanslama teknolojilerinin yaygınlaşması ve biyolojik verilerin çoğalması ile beraber DNA ve protein dizi hizalama algoritmalarının daha yüksek performans ile calıştırılmasına olan ihtiyaç artmıştır. Bu çalışma iki iyi bilinen, Needleman-Wunsch ve Smith-Waterman, DNA ve Protein dizi hizalama algoritmalarının Python programlama dilinde farklı derlenme stratejilerinin sistematik kıyaslamasıdır. Sıkça kullanılan Biopython’un ikili hizalama modülü ile kendi yazdığımız yazılımın farklı derleme yaklaşımlarının performans farkının kıyaslanması amaçlanmıştır. Sonuçlar Numba’nın just-in-time derleme yönteminin PyPy ve Cython derleme yöntemleri ya da Biopython modülüne kıyasla genel olarak daha yüksek performans gösterdiğini ortaya koymuştur. Bu çalışmanın geniş çapta dizi hizalama gerektiren yazılım protipleme çalışmalarında verimliliği arttıracağı düşünülmektedir.Article Triplex-Forming Dna Probe Approach for Silver Detection and the Effect of C-G·c Triplet Distribution on Triplex Stability(2019-12-31) Doluca, OsmanIn this study novel triplex forming DNA probes have been designed in order to detect Ag+ ion in low concentrations. The use of triplex forming oligonucleotides is a convenient in applications of sensing biomolecules due to their sequence specificity and programmability. However, the use of triplexes has its own obstacles. While antiparallel triplex forming sequences tend to prefer G-quadruplex formation over triplexes, parallel triplexes are also challenging because their formation is triggered by lowering the pH, or using of high concentrations of cations for the stabilization of C-G·C triplets, ie. Ag+. While due to electrostatic forces C-G·C triplets stabilize in the presence of cations, this limits possible choices for a triplex forming sequence. A better understanding of the impact of the sequence and designing accordingly may improve the stability of a triplex and lower the need for high cation concentration. Here we have present Triplex-forming DNA-based probes with different distributions of C-G·C triplets for detection of Ag+ and show the impact of the C-G·C triplet distribution on the stability of parallel triplexes. Our results indicate Ag+ detection as low as 20 nM and show dramatic increase in stability when C-G·C triplets are positioned at the flanks of the triplex.Article Citation - WoS: 1G-Quadruplex Enrichment Analysis Reveals Their Role as Intronic Regulatory Elements in Plants(Tubitak Scientific & Technical Research Council Turkey, 2019-03-07) Doluca, OsmanG-Quadruplexes, a class of noncanonical but highly stable nucleic acid structures, have the potential to be part of the regulatory mechanism of cells. They can form in the genome where the double-stranded helix is unwound to facilitate formation of a G-quadruplex. The biological significance of these structures is yet to be understood entirely. This work presents a novel approach and investigates common characteristics in the distribution of G-quadruplexes relative to genes in plants through analysis of genomes and gene expressions. The results indicate that G-quadruplex distribution has gone through significant changes with the evolution of higher plants and, for the first tune, that G-quadruplexes enriched at the beginning of introns may have a regulatory role during transcription.