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Probability calculations of orthologous genes
University of Skövde, School of Humanities and Informatics.
2005 (English)Independent thesis Basic level (degree of Bachelor)Student thesis
Abstract [en]

The aim of this thesis is to formulate and implement an algorithm that calculates the probability for two genes being orthologs, given a gene tree and a species tree. To do this, reconciliations between the gene tree and the species trees are used. A birth and death process is used to model the evolution, and used to calculate the orthology probability. The birth and death parameters are approximated with a Markov Chain Monte Carlo (MCMC). A MCMC framework for probability calculations of reconciliations written by Arvestad et al. (2003) is used. Rules for orthologous reconciliations are developed and implemented to calculate the probability for the reconciliations that have two genes as orthologs. The rules where integrated with the Arvestad et al. (2003) framework, and the algorithm was then validated and tested.

Place, publisher, year, edition, pages
Skövde: Institutionen för kommunikation och information , 2005. , 53 p.
Keyword [en]
Phylogeny, Reconciliation, Orthology, Birth and Death process, Markov Chain Monte Carlo
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:his:diva-972OAI: oai:DiVA.org:his-972DiVA: diva2:3398
Presentation
(English)
Uppsok
Life Earth Science
Supervisors
Available from: 2008-03-19 Created: 2008-03-19 Last updated: 2009-10-21

Open Access in DiVA

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CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf