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Full-Text Articles in Computer Engineering
Biological Sequence Simulation For Testing Complex Evolutionary Hypotheses: Indel-Seq-Gen Version 2.0, Cory L. Strope
Biological Sequence Simulation For Testing Complex Evolutionary Hypotheses: Indel-Seq-Gen Version 2.0, Cory L. Strope
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
Reconstructing the evolutionary history of biological sequences will provide a better understanding of mechanisms of sequence divergence and functional evolution. Long-term sequence evolution includes not only substitutions of residues but also more dynamic changes such as insertion, deletion, and long-range rearrangements. Such dynamic changes make reconstructing sequence evolution history difficult and affect the accuracy of molecular evolutionary methods, such as multiple sequence alignments (MSAs) and phylogenetic methods. In order to test the accuracy of these methods, benchmark datasets are required. However, currently available benchmark datasets have limitations in their sizes and evolutionary histories of the included sequences are unknown. These …
Classification, Clustering And Data-Mining Of Biological Data, Thomas Triplet
Classification, Clustering And Data-Mining Of Biological Data, Thomas Triplet
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are currently over 1100 molecular biology databases dispersed throughout the Internet. However, very few of them integrate data from multiple sources. To assist in the functional and evolutionary analysis of the abundant number of novel proteins, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database that integrates data from various biological sources. PROFESS is freely available athttp://cse.unl.edu/~profess/. Our database is designed to be versatile and expandable and will not …
Gene Order Phylogeny And The Evolution Of Methanogens, Haiwei Luo, Zhiyi Sun, William Arndt, Jian Shi, Robert Friedman, Jijun Tang
Gene Order Phylogeny And The Evolution Of Methanogens, Haiwei Luo, Zhiyi Sun, William Arndt, Jian Shi, Robert Friedman, Jijun Tang
Faculty Publications
Methanogens are a phylogenetically diverse group belonging to Euryarchaeota. Previously, phylogenetic approaches using large datasets revealed that methanogens can be grouped into two classes, “Class I” and “Class II”. However, some deep relationships were not resolved. For instance, the monophyly of “Class I” methanogens, which consist of Methanopyrales, Methanobacteriales and Methanococcales, is disputable due to weak statistical support. In this study, we use MSOAR to identify common orthologous genes from eight methanogen species and a Thermococcale species (outgroup), and apply GRAPPA and FastME to compute distance-based gene order phylogeny. The gene order phylogeny supports two classes of methanogens, but it …
Gathering Cows Using Virtual Fencing Methodologies, Dean M. Anderson, Marek Doniec, Carrick Detweiler, Iuliu Vesilescu, Daniela Rus, Barbara Nolen, Roy Libeau
Gathering Cows Using Virtual Fencing Methodologies, Dean M. Anderson, Marek Doniec, Carrick Detweiler, Iuliu Vesilescu, Daniela Rus, Barbara Nolen, Roy Libeau
CSE Conference and Workshop Papers
Free-ranging livestock are classically controlled by herders. Holding, moving, or gathering free-ranging cattle requires flexible husbandry practices for efficient and effective lowstress animal management. Behavioral theory and practical experience indicates cattle can be taught to respond to auditory cues. Preliminary research has demonstrated that cows can be gathered autonomously using recorded audio cues associated with manual gathering. However, efficient gathering requires movement in the proper direction. Therefore, we believe using audio cues administered from directional virtual fencing (DVF™) equipment can facilitate proper animal orientation and facilitate the gathering of animals with minimal human intervention. Results from applying directional audio cues …