Physical Sciences and Mathematics Commons^™

Fast Program For Sequence Alignment Using Partition Function Posterior Probabilities, Meera Prasad

Theses

The key requirements of a good sequence alignment tool are high accuracy and fast execution. The existing Probalign program is a highly accurate tool for sequence alignment of both proteins and nucleotides. However, the time for execution is fairly high. The focus is therefore, to reduce the running time of the existing version of Probalign, maintaining its current accuracy level.

The thesis conducts a detail analysis of the performance of Probalign to bring down the running time of the existing code. A modified version of Probalign, Version 1.4 is released. A new program for sequence alignment with faster computation is …

Ranking Single Nucleotide Polymorphisms With Support Vector Regression In Continuous Phenotypes, Seif Shahidain

Theses

Support vector machines (SVM) have been used to improve the ranking of single nucleotide polymorphisms (SNPs) over traditional chi-square tests in disease case studies [2]. In this investigation, ranking SNPs with support vector regression (SVR) was compared to the Wald test in predicting continuous phenotypes. SVR-ranked SNPs consistently outperformed the Wald test-ranked SNPs to provide a more accurate prediction of the phenotype with fewer SNPs across several methods of prediction.

Dynamic-Parinet (D-Parinet) : Indexing Present And Future Trajectories In Networks, Mou Nandi

Theses

While indexing historical trajectories is a hot topic in the field of moving objects (MO) databases for many years, only a few of them consider that the objects movements are constrained. DYNAMIC-PARINET (D-PATINET) is designed for capturing of trajectory data flow in multiple discrete small time interval efficiently and to predict a MO’s movement or the underlying network state at a future time.

The cornerstone of D-PARINET is PARINET, an efficient index for historical trajectory data. The structure of PARINET is based on a combination of graph partitioning and a set of composite B+-tree local indexes tuned for a given …

Aminormotiffinder - A Graph Grammar Based Tool To Effectively Search A Minor Motifs In 3d Rna Molecules, Ankur Malhotra

Theses

RNA Motifs are three dimensional folds that play important role in RNA folding and its interaction with other molecules. They basically have modular structure and are composed of conserved building blocks dependent upon the sequence. Their automated in silico identification remains a challenging task. Existing motif identification tools does not correctly identify motifs with large structure variations. Here a “graph rewriting” based method is proposed to identify motifs in real three dimensional structures. The unique encoding of A Minor Searcher takes into consideration the non canonical base pairs and also multipairing of RNA structural motifs. The accuracy is demonstrated by …