Exploration of natural alignment scoring rules and clustering thresholds for bacterial core/pan genome analysis

L. Albayrak, K. Khanipov, M. Rojas, George Golovko, M. Pimenova, Yuriy Fofanov, M. Kosoy

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Bacterial adaptation through gene loss and acquisition are the fundamental mechanisms that determine the structure of the core and pan genomes. One of the challenges in identifying homologous genes required for the description of core and pan genomes is the absence of appropriate alignment scoring rules and clustering thresholds. In this work, we present new methods to establish appropriate alignment scoring rules and clustering thresholds.

Original languageEnglish (US)
Title of host publicationProceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages249-254
Number of pages6
Volume2018-January
ISBN (Electronic)9781538613245
DOIs
StatePublished - Jan 8 2018
Event17th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2017 - Herndon, United States
Duration: Oct 23 2017Oct 25 2017

Other

Other17th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2017
CountryUnited States
CityHerndon
Period10/23/1710/25/17

Fingerprint

Scoring
Cluster Analysis
Genome
Alignment
Genes
Clustering
Gene
Acquisition

Keywords

  • Alignment score
  • Bioinformatics
  • Clustering
  • Core genome
  • Gene profiles
  • Pan genome
  • Sequence alignment

ASJC Scopus subject areas

  • Information Systems
  • Biomedical Engineering
  • Modeling and Simulation
  • Signal Processing
  • Health Informatics

Cite this

Albayrak, L., Khanipov, K., Rojas, M., Golovko, G., Pimenova, M., Fofanov, Y., & Kosoy, M. (2018). Exploration of natural alignment scoring rules and clustering thresholds for bacterial core/pan genome analysis. In Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017 (Vol. 2018-January, pp. 249-254). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBE.2017.00-46

Exploration of natural alignment scoring rules and clustering thresholds for bacterial core/pan genome analysis. / Albayrak, L.; Khanipov, K.; Rojas, M.; Golovko, George; Pimenova, M.; Fofanov, Yuriy; Kosoy, M.

Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017. Vol. 2018-January Institute of Electrical and Electronics Engineers Inc., 2018. p. 249-254.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Albayrak, L, Khanipov, K, Rojas, M, Golovko, G, Pimenova, M, Fofanov, Y & Kosoy, M 2018, Exploration of natural alignment scoring rules and clustering thresholds for bacterial core/pan genome analysis. in Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017. vol. 2018-January, Institute of Electrical and Electronics Engineers Inc., pp. 249-254, 17th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2017, Herndon, United States, 10/23/17. https://doi.org/10.1109/BIBE.2017.00-46
Albayrak L, Khanipov K, Rojas M, Golovko G, Pimenova M, Fofanov Y et al. Exploration of natural alignment scoring rules and clustering thresholds for bacterial core/pan genome analysis. In Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017. Vol. 2018-January. Institute of Electrical and Electronics Engineers Inc. 2018. p. 249-254 https://doi.org/10.1109/BIBE.2017.00-46
Albayrak, L. ; Khanipov, K. ; Rojas, M. ; Golovko, George ; Pimenova, M. ; Fofanov, Yuriy ; Kosoy, M. / Exploration of natural alignment scoring rules and clustering thresholds for bacterial core/pan genome analysis. Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017. Vol. 2018-January Institute of Electrical and Electronics Engineers Inc., 2018. pp. 249-254
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