Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to strong similarities that are not homologies. Standard repeat-masking methods fail to eliminate this problem, and they are especially ill-suited to AT-rich DNA such as malaria and slime-mould genomes. We present a new repeat-masking method, TAN...

We show that if a Legendrian knot in standard contact R3 possesses a generating family then there exists an augmentation of the Chekanov-Eliashberg DGA so that the associated linearized contact homology is isomorphic to singular homology groups arising from the generating family. We discuss the relationship between normal rulings, augmentations, and generating families. In particular, we provid...

Abstract Appropriately representing elements in a database so that queries may be accurately matched is central task information retrieval; recently, this has been achieved by embedding the graphical structure of into manifold hierarchy-preserving manner using variety metrics. Persistent homology tool commonly used topological data analysis able to rigorously characterize terms both its hierarc...

Persistent homology is typically computed through persistent cohomology. While this generally improves the running time significantly, it does not facilitate extraction of representatives. The mentioned representatives are geometric manifestations corresponding holes and often carry desirable information.We propose a new method using In summary, we first compute cohomology use obtained informat...

background: lipophosphoglycan 3 (lpg3) is required for the lpg assembly, a well known virulent molecule. in this study, the lpg3 gene of the lizard and mammalian leishmania species were cloned and sequenced. a three-dimensional structure (3d) for the target sequence was also predicted by comparative (homology) modeling. materials and methods: an optimization pcr amplification was performed on g...

background: luxi is a component of the quorum sensing signaling pathway in vibrio fischeri responsible for the inducer synthesis that is essential for bioluminescence. methods: homology modeling of luxi was carried out using phyre2 and refined with the galaxyweb server. five models were generated and evaluated by errat, anolea, qmean6, and procheck. results: five refined models were generated b...

medicinal use of the opium poppy (papaver somniferum l) has ancient history, but the isolation of morphine was not described until the early nineteenth century. morphine is the most important alkaloid of opium poppy in the last 50 years. in the morphine pathway has been reported to generate morphine in this species, codm has a crucial role as the gene coding the enzyme responsible for demethyla...

We provide a translation between Chekanov’s combinatorial theory for invariants of Legendrian knots in the standard contact R and a relative version of Eliashberg and Hofer’s contact homology. We use this translation to transport the idea of “coherent orientations” from the contact homology world to Chekanov’s combinatorial setting. As a result, we obtain a lifting of Chekanov’s differential gr...

Triangulation is a convenient tool to consider when we are determining some properties of a topological space. Specifically, we can compute the homology and cohomology groups using the simplicial homology and cohomology of the triangulated space which is much easier than involving more complicated theories. In this paper, we will review the standard proof by Radó of the existence of triangulati...

In this paper we focus on preprocessing for persistent homology computations. We adapt some techniques that were successfully used for standard homology computations. The main idea is to reduce the complex prior to generating its boundary matrix, which is costly to store and process. We discuss the following reduction methods: elementary collapses, coreductions (as defined by Mrozek and Batko),...