Kunzmann, Patrick (2023)
Development of a programming library for general bioinformatics.
Technische Universität Darmstadt
doi: 10.26083/tuprints-00024784
Dissertation, Erstveröffentlichung, Verlagsversion
Kurzbeschreibung (Abstract)
Bioinformatics progresses at an unprecedented pace. At the same time the software implementing the essential algorithms is often incompatible with each other in terms of data input and output. In consequence it can require substantial effort to establish a workflow that combines different programs. Furthermore, the flexibility of such software is usually limited to a relatively small number of options. These circumstances hamper the adaption of these programs to new problems. An alternative approach to command line programs are programming libraries, that enable the user to apply already implemented algorithms and at the same time to harness the full feature spectrum of a programming language.
In this thesis the Python bioinformatics package Biotite is presented. It unifies popular algorithms from sequence and structure analysis into a flexible library, which is applicable to a wide range of biological questions. Furthermore, new algorithms are presented, enhancing the bioinformatician’s toolkit with a novel sequence alignment visualization approach and universally applicable hydrogen prediction method. Finally, via the application of Biotite this thesis provides new insights into the molecular mechanism of cation channels and novel evaluation methods for sequencing data from SELEX experiments.
| Typ des Eintrags: | Dissertation | ||||
|---|---|---|---|---|---|
| Erschienen: | 2023 | ||||
| Autor(en): | Kunzmann, Patrick | ||||
| Art des Eintrags: | Erstveröffentlichung | ||||
| Titel: | Development of a programming library for general bioinformatics | ||||
| Sprache: | Englisch | ||||
| Referenten: | Hamacher, Prof. Dr. Kay ; Süß, Prof. Dr. Beatrix | ||||
| Publikationsjahr: | 5 Dezember 2023 | ||||
| Ort: | Darmstadt | ||||
| Kollation: | 175 Seiten in verschiedenen Zählungen | ||||
| Datum der mündlichen Prüfung: | 9 März 2023 | ||||
| DOI: | 10.26083/tuprints-00024784 | ||||
| URL / URN: | https://tuprints.ulb.tu-darmstadt.de/24784 | ||||
| Kurzbeschreibung (Abstract): | Bioinformatics progresses at an unprecedented pace. At the same time the software implementing the essential algorithms is often incompatible with each other in terms of data input and output. In consequence it can require substantial effort to establish a workflow that combines different programs. Furthermore, the flexibility of such software is usually limited to a relatively small number of options. These circumstances hamper the adaption of these programs to new problems. An alternative approach to command line programs are programming libraries, that enable the user to apply already implemented algorithms and at the same time to harness the full feature spectrum of a programming language. In this thesis the Python bioinformatics package Biotite is presented. It unifies popular algorithms from sequence and structure analysis into a flexible library, which is applicable to a wide range of biological questions. Furthermore, new algorithms are presented, enhancing the bioinformatician’s toolkit with a novel sequence alignment visualization approach and universally applicable hydrogen prediction method. Finally, via the application of Biotite this thesis provides new insights into the molecular mechanism of cation channels and novel evaluation methods for sequencing data from SELEX experiments. |
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| Alternatives oder übersetztes Abstract: |
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| Status: | Verlagsversion | ||||
| URN: | urn:nbn:de:tuda-tuprints-247849 | ||||
| Sachgruppe der Dewey Dezimalklassifikatin (DDC): | 000 Allgemeines, Informatik, Informationswissenschaft > 004 Informatik 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie |
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| Fachbereich(e)/-gebiet(e): | 10 Fachbereich Biologie 10 Fachbereich Biologie > Computational Biology and Simulation |
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| Hinterlegungsdatum: | 05 Dez 2023 13:04 | ||||
| Letzte Änderung: | 06 Dez 2023 08:06 | ||||
| PPN: | |||||
| Referenten: | Hamacher, Prof. Dr. Kay ; Süß, Prof. Dr. Beatrix | ||||
| Datum der mündlichen Prüfung / Verteidigung / mdl. Prüfung: | 9 März 2023 | ||||
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| Suche nach Titel in: | TUfind oder in Google | ||||
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