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Consemblex: A Consensus-Based Transcriptome Assembly Approach That Extends Consemble And Improves Transcriptome Assembly, Richard Mwaba
Consemblex: A Consensus-Based Transcriptome Assembly Approach That Extends Consemble And Improves Transcriptome Assembly, Richard Mwaba
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
An accurate transcriptome is essential to understanding biological systems enabling omics analyses such as gene expression, gene discovery, and gene-regulatory network construction. However, assembling an accurate transcriptome is challenging, especially for organisms without adequate reference genomes or transcriptomes. While several methods for transcriptome assembly with different approaches exist, it is still difficult to establish the most accurate methods. This thesis explores the different transcriptome assembly methods and compares their performances using simulated benchmark transcriptomes with varying complexity. We also introduce ConSemblEX to improve a consensus-based ensemble transcriptome assembler, ConSemble, in three main areas: we provide the ability to use any …
Suffix Tree, Minwise Hashing And Streaming Algorithms For Big Data Analysis In Bioinformatics, Sairam Behera
Suffix Tree, Minwise Hashing And Streaming Algorithms For Big Data Analysis In Bioinformatics, Sairam Behera
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
In this dissertation, we worked on several algorithmic problems in bioinformatics using mainly three approaches: (a) a streaming model, (b) sux-tree based indexing, and (c) minwise-hashing (minhash) and locality-sensitive hashing (LSH). The streaming models are useful for large data problems where a good approximation needs to be achieved with limited space usage. We developed an approximation algorithm (Kmer-Estimate) using the streaming approach to obtain a better estimation of the frequency of k-mer counts. A k-mer, a subsequence of length k, plays an important role in many bioinformatics analyses such as genome distance estimation. We also developed new methods that use …
Consensus Ensemble Approaches Improve De Novo Transcriptome Assemblies, Adam Voshall
Consensus Ensemble Approaches Improve De Novo Transcriptome Assemblies, Adam Voshall
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
Accurate and comprehensive transcriptome assemblies lay the foundation for a range of analyses, such as differential gene expression analysis, metabolic pathway reconstruction, novel gene discovery, or metabolic flux analysis. With the arrival of next-generation sequencing technologies it has become possible to acquire the whole transcriptome data rapidly even from non-model organisms. However, the problem of accurately assembling the transcriptome for any given sample remains extremely challenging, especially in species with a high prevalence of recent gene or genome duplications, those with alternative splicing of transcripts, or those whose genomes are not well studied. This thesis provides a detailed overview of …