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Expected Gene Order Distances and Model Selection in Bacteria

Daniel Dalevi (Institutionen för data- och informationsteknik, Datavetenskap, Bioinformatik (Chalmers)) ; Niklas Eriksen (Institutionen för matematiska vetenskaper, matematik)
Proceedings of German Conference on Bioinformatics, Potsdam, 26-28 september, 2007, LNI (1617-5468). Vol. 115 (2007), p. 135-144.
[Konferensbidrag, refereegranskat]

The most parsimonous distances calculated in pairwise gene order comparisons cannot accurately reflect the true number of events separating two species, unless the number of changes are few. Better is to use the expected distances. In this study we recapitulate previous results and derive new expected distances for models that have gained support in other studies, such as, symmetrical reversal distances and short reversals. Further, we investigate the patterns of dotplots between species of bacteria with the purpose of model selection in gene order problems. We find several categories of data which can be explained by carefully weighing the contributions of reversals, transpositions, symmetric reversals, single gene transpositions, and single gene reversals.

Nyckelord: reversal, inversion, transposition, gene order rearrangement, method of moments estimate



Denna post skapades 2007-10-23.
CPL Pubid: 56672

 

Institutioner (Chalmers)

Institutionen för data- och informationsteknik, Datavetenskap, Bioinformatik (Chalmers)
Institutionen för matematiska vetenskaper, matematik (2005-2016)

Ämnesområden

Diskret matematik
Teoretisk datalogi
Bioinformatik och systembiologi

Chalmers infrastruktur