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Articles 1 - 6 of 6
Full-Text Articles in Computational Biology
Creation Of A Digital Storage System For Genome Sequencing Metadata, Jacquelin W. Olexa
Creation Of A Digital Storage System For Genome Sequencing Metadata, Jacquelin W. Olexa
Undergraduate Theses, Professional Papers, and Capstone Artifacts
As the field of computational genomics continues to expand in both potential and application, it is now more imperative than ever to ensure that massive genetic sequencing datasets are properly stored in an accessible manner. This project sought to establish a practical, user-friendly, secure system for a genomics research lab (the Good Lab; thegoodlab.org) at the University of Montana. A MySQL database and connected web application was ruled the best configuration to maximize utility and accessibility for the lab’s researchers. Building the logical framework for the database, creating the server, and sourcing data occurred over several months. The dataset ranged …
An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy, Christopher L. Pierpont
An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy, Christopher L. Pierpont
Graduate Student Theses, Dissertations, & Professional Papers
Thermophilic microorganisms have been scientifically observed since the early nineteenth century and have spurred many questions about the limits of life and the capacity of organisms to survive extreme conditions. Decades of research on thermophile proteins and genomes have yielded several proposed correlates of temperature that may contribute to adaptation of bacteria and archaea to high temperature. However, many of the generalizations reported are drawn from analyses of deeply divergent taxa or from individual case studies in isolation from mesophilic relatives. Members of the Synechococcus A/B (SynAB) group are the only cyanobacteria with members able to grow above 65 °C …
Fathmm: Frameshift Aware Translated Hidden Markov Models, Genevieve Krause
Fathmm: Frameshift Aware Translated Hidden Markov Models, Genevieve Krause
Graduate Student Theses, Dissertations, & Professional Papers
No abstract provided.
Sparse Forward-Backward Alignment For Sensitive Database Search With Small Memory And Time Requirements, David H. Rich
Sparse Forward-Backward Alignment For Sensitive Database Search With Small Memory And Time Requirements, David H. Rich
Graduate Student Theses, Dissertations, & Professional Papers
Sequence annotation is typically performed by aligning an unlabeled sequence to a collection of known sequences, with the aim of identifying non-random similarities. Given the broad diversity of new sequences and the considerable scale of modern sequence databases, there is significant tension between the competing needs for sensitivity and speed, with multiple tools displacing the venerable BLAST software suite on one axis or another. In recent years, alignment based on profile hidden Markov models (pHMMs) and associated probabilistic inference methods have demonstrated increased sensitivity due in part to consideration of the ensemble of all possible alignments between a query and …
Ensemble Protein Inference Evaluation, Kyle Lee Lucke
Ensemble Protein Inference Evaluation, Kyle Lee Lucke
Graduate Student Theses, Dissertations, & Professional Papers
The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …
K-Mer Analysis Pipeline For Classification Of Dna Sequences From Metagenomic Samples, Russell Kaehler
K-Mer Analysis Pipeline For Classification Of Dna Sequences From Metagenomic Samples, Russell Kaehler
Graduate Student Theses, Dissertations, & Professional Papers
Biological sequence datasets are increasing at a prodigious rate. The volume of data in these datasets surpasses what is observed in many other fields of science. New developments wherein metagenomic DNA from complex bacterial communities is recovered and sequenced are producing a new kind of data known as metagenomic data, which is comprised of DNA fragments from many genomes. Developing a utility to analyze such metagenomic data and predict the sample class from which it originated has many possible implications for ecological and medical applications. Within this document is a description of a series of analytical techniques used to process …