A "Long Indel" model for evolutionary sequence alignment.

We present a new probabilistic model of sequence evolution, allowing indels of arbitrary length, and give sequence alignment algorithms for our model. Previously implemented evolutionary models have allowed (at most) single-residue indels or have introduced artifacts such as the existence of indivis...

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Үндсэн зохиолчид: Miklós, I, Lunter, G, Holmes, I
Формат: Journal article
Хэл сонгох:English
Хэвлэсэн: 2004
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author Miklós, I
Lunter, G
Holmes, I
author_facet Miklós, I
Lunter, G
Holmes, I
author_sort Miklós, I
collection OXFORD
description We present a new probabilistic model of sequence evolution, allowing indels of arbitrary length, and give sequence alignment algorithms for our model. Previously implemented evolutionary models have allowed (at most) single-residue indels or have introduced artifacts such as the existence of indivisible "fragments." We compare our algorithm to these previous methods by applying it to the structural homology dataset HOMSTRAD, evaluating the accuracy of (1) alignments and (2) evolutionary time estimates. With our method, it is possible (for the first time) to integrate probabilistic sequence alignment, with reliability indicators and arbitrary gap penalties, in the same framework as phylogenetic reconstruction. Our alignment algorithm requires that we evaluate the likelihood of any specific path of mutation events in a continuous-time Markov model, with the event times integrated out. To this effect, we introduce a "trajectory likelihood" algorithm (Appendix A). We anticipate that this algorithm will be useful in more general contexts, such as Markov Chain Monte Carlo simulations.
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spelling oxford-uuid:ea1a6c7f-2ec9-4e20-af08-a2fd943a743a2022-03-27T10:59:11ZA "Long Indel" model for evolutionary sequence alignment.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:ea1a6c7f-2ec9-4e20-af08-a2fd943a743aEnglishSymplectic Elements at Oxford2004Miklós, ILunter, GHolmes, IWe present a new probabilistic model of sequence evolution, allowing indels of arbitrary length, and give sequence alignment algorithms for our model. Previously implemented evolutionary models have allowed (at most) single-residue indels or have introduced artifacts such as the existence of indivisible "fragments." We compare our algorithm to these previous methods by applying it to the structural homology dataset HOMSTRAD, evaluating the accuracy of (1) alignments and (2) evolutionary time estimates. With our method, it is possible (for the first time) to integrate probabilistic sequence alignment, with reliability indicators and arbitrary gap penalties, in the same framework as phylogenetic reconstruction. Our alignment algorithm requires that we evaluate the likelihood of any specific path of mutation events in a continuous-time Markov model, with the event times integrated out. To this effect, we introduce a "trajectory likelihood" algorithm (Appendix A). We anticipate that this algorithm will be useful in more general contexts, such as Markov Chain Monte Carlo simulations.
spellingShingle Miklós, I
Lunter, G
Holmes, I
A "Long Indel" model for evolutionary sequence alignment.
title A "Long Indel" model for evolutionary sequence alignment.
title_full A "Long Indel" model for evolutionary sequence alignment.
title_fullStr A "Long Indel" model for evolutionary sequence alignment.
title_full_unstemmed A "Long Indel" model for evolutionary sequence alignment.
title_short A "Long Indel" model for evolutionary sequence alignment.
title_sort long indel model for evolutionary sequence alignment
work_keys_str_mv AT miklosi alongindelmodelforevolutionarysequencealignment
AT lunterg alongindelmodelforevolutionarysequencealignment
AT holmesi alongindelmodelforevolutionarysequencealignment
AT miklosi longindelmodelforevolutionarysequencealignment
AT lunterg longindelmodelforevolutionarysequencealignment
AT holmesi longindelmodelforevolutionarysequencealignment