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...
| Päätekijät: | , , |
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| Aineistotyyppi: | Journal article |
| Kieli: | English |
| Julkaistu: |
2004
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| _version_ | 1826302911275073536 |
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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. |
| first_indexed | 2024-03-07T05:54:38Z |
| format | Journal article |
| id | oxford-uuid:ea1a6c7f-2ec9-4e20-af08-a2fd943a743a |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T05:54:38Z |
| publishDate | 2004 |
| record_format | dspace |
| 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 |