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Full-Text Articles in Physical Sciences and Mathematics
Comparative Analyses Of De Novo Transcriptome Assembly Pipelines For Diploid Wheat, Natasha Pavlovikj
Comparative Analyses Of De Novo Transcriptome Assembly Pipelines For Diploid Wheat, Natasha Pavlovikj
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
Gene expression and transcriptome analysis are currently one of the main focuses of research for a great number of scientists. However, the assembly of raw sequence data to obtain a draft transcriptome of an organism is a complex multi-stage process usually composed of pre-processing, assembling, and post-processing. Each of these stages includes multiple steps such as data cleaning, error correction and assembly validation. Different combinations of steps, as well as different computational methods for the same step, generate transcriptome assemblies with different accuracy. Thus, using a combination that generates more accurate assemblies is crucial for any novel biological discoveries. Implementing …
Formal Concept Analysis Applications In Bioinformatics, Sarah Roscoe
Formal Concept Analysis Applications In Bioinformatics, Sarah Roscoe
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
Bioinformatics is an important field that seeks to solve biological problems with the help of computation. One specific field in bioinformatics is that of genomics, the study of genes and their functions. Genomics can provide valuable analysis as to the interaction between how genes interact with their environment. One such way to measure the interaction is through gene expression data, which determines whether (and how much) a certain gene activates in a situation. Analyzing this data can be critical for predicting diseases or other biological reactions. One method used for analysis is Formal Concept Analysis (FCA), a computing technique based …
Application Of Cosine Similarity In Bioinformatics, Srikanth Maturu
Application Of Cosine Similarity In Bioinformatics, Srikanth Maturu
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
Finding similar sequences to an input query sequence (DNA or proteins) from a sequence data set is an important problem in bioinformatics. It provides researchers an intuition of what could be related or how the search space can be reduced for further tasks. An exact brute-force nearest-neighbor algorithm used for this task has complexity O(m * n) where n is the database size and m is the query size. Such an algorithm faces time-complexity issues as the database and query sizes increase. Furthermore, the use of alignment-based similarity measures such as minimum edit distance adds an additional complexity to the …