FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4286562021> ?p ?o ?g. }

• W4286562021 endingPage "318" @default.
• W4286562021 startingPage "307" @default.
• W4286562021 abstract "Abstract Modern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present-day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study biological processes such as adaptation and convergent evolution across a variety of applications. Here, we propose a dynamic programming algorithm for fast joint likelihood-based reconstruction of ancestral sequences under the Poisson Indel Process (PIP). Unlike previous approaches, our method, named ARPIP, enables the reconstruction with insertions and deletions based on an explicit indel model. Consequently, inferred indel events have an explicit biological interpretation. Likelihood computation is achieved in linear time with respect to the number of sequences. Our method consists of two steps, namely finding the most probable indel points and reconstructing ancestral sequences. First, we find the most likely indel points and prune the phylogeny to reflect the insertion and deletion events per site. Second, we infer the ancestral states on the pruned subtree in a manner similar to FastML. We applied ARPIP (Ancestral Reconstruction under PIP) on simulated data sets and on real data from the Betacoronavirus genus. ARPIP reconstructs both the indel events and substitutions with a high degree of accuracy. Our method fares well when compared to established state-of-the-art methods such as FastML and PAML. Moreover, the method can be extended to explore both optimal and suboptimal reconstructions, include rate heterogeneity through time and more. We believe it will expand the range of novel applications of ancestral sequence reconstruction. [Ancestral sequences; dynamic programming; evolutionary stochastic process; indel; joint ancestral sequence reconstruction; maximum likelihood; Poisson Indel Process; phylogeny; SARS-CoV.]" @default.
• W4286562021 created "2022-07-22" @default.
• W4286562021 creator A5020826103 @default.
• W4286562021 creator A5029417733 @default.
• W4286562021 creator A5044226183 @default.
• W4286562021 creator A5046692009 @default.
• W4286562021 creator A5085414073 @default.
• W4286562021 date "2022-07-22" @default.
• W4286562021 modified "2023-09-30" @default.
• W4286562021 title "ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process" @default.
• W4286562021 cites W128985141 @default.
• W4286562021 cites W1536490017 @default.
• W4286562021 cites W2007203150 @default.
• W4286562021 cites W2013404472 @default.
• W4286562021 cites W2021839440 @default.
• W4286562021 cites W2038978937 @default.
• W4286562021 cites W2046457574 @default.
• W4286562021 cites W2062018285 @default.
• W4286562021 cites W2064394080 @default.
• W4286562021 cites W2065400176 @default.
• W4286562021 cites W2065461553 @default.
• W4286562021 cites W2070579299 @default.
• W4286562021 cites W2077564233 @default.
• W4286562021 cites W2090748603 @default.
• W4286562021 cites W2092979861 @default.
• W4286562021 cites W2102424972 @default.
• W4286562021 cites W2105149323 @default.
• W4286562021 cites W2108795433 @default.
• W4286562021 cites W2109028614 @default.
• W4286562021 cites W2110335151 @default.
• W4286562021 cites W2111211467 @default.
• W4286562021 cites W2111762123 @default.
• W4286562021 cites W2114525641 @default.
• W4286562021 cites W2117884309 @default.
• W4286562021 cites W2119632499 @default.
• W4286562021 cites W2144606496 @default.
• W4286562021 cites W2150090955 @default.
• W4286562021 cites W2155761693 @default.
• W4286562021 cites W2157552136 @default.
• W4286562021 cites W2167504240 @default.
• W4286562021 cites W2524916784 @default.
• W4286562021 cites W2610994034 @default.
• W4286562021 cites W2763547223 @default.
• W4286562021 cites W2890963022 @default.
• W4286562021 cites W3012764845 @default.
• W4286562021 cites W3112376646 @default.
• W4286562021 cites W3189492453 @default.
• W4286562021 cites W3204274894 @default.
• W4286562021 cites W3209726119 @default.
• W4286562021 cites W4225395139 @default.
• W4286562021 cites W4250847479 @default.
• W4286562021 cites W638482479 @default.
• W4286562021 doi "https://doi.org/10.1093/sysbio/syac050" @default.
• W4286562021 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/35866991" @default.
• W4286562021 hasPublicationYear "2022" @default.
• W4286562021 type Work @default.
• W4286562021 citedByCount "0" @default.
• W4286562021 crossrefType "journal-article" @default.
• W4286562021 hasAuthorship W4286562021A5020826103 @default.
• W4286562021 hasAuthorship W4286562021A5029417733 @default.
• W4286562021 hasAuthorship W4286562021A5044226183 @default.
• W4286562021 hasAuthorship W4286562021A5046692009 @default.
• W4286562021 hasAuthorship W4286562021A5085414073 @default.
• W4286562021 hasBestOaLocation W42865620211 @default.
• W4286562021 hasConcept C104317684 @default.
• W4286562021 hasConcept C11413529 @default.
• W4286562021 hasConcept C119054055 @default.
• W4286562021 hasConcept C135763542 @default.
• W4286562021 hasConcept C153209595 @default.
• W4286562021 hasConcept C154945302 @default.
• W4286562021 hasConcept C167625842 @default.
• W4286562021 hasConcept C193252679 @default.
• W4286562021 hasConcept C2776214188 @default.
• W4286562021 hasConcept C2778112365 @default.
• W4286562021 hasConcept C2910714999 @default.
• W4286562021 hasConcept C41008148 @default.
• W4286562021 hasConcept C45484198 @default.
• W4286562021 hasConcept C54355233 @default.
• W4286562021 hasConcept C62142553 @default.
• W4286562021 hasConcept C70721500 @default.
• W4286562021 hasConcept C78458016 @default.
• W4286562021 hasConcept C86803240 @default.
• W4286562021 hasConcept C88031987 @default.
• W4286562021 hasConcept C90132467 @default.
• W4286562021 hasConceptScore W4286562021C104317684 @default.
• W4286562021 hasConceptScore W4286562021C11413529 @default.
• W4286562021 hasConceptScore W4286562021C119054055 @default.
• W4286562021 hasConceptScore W4286562021C135763542 @default.
• W4286562021 hasConceptScore W4286562021C153209595 @default.
• W4286562021 hasConceptScore W4286562021C154945302 @default.
• W4286562021 hasConceptScore W4286562021C167625842 @default.
• W4286562021 hasConceptScore W4286562021C193252679 @default.
• W4286562021 hasConceptScore W4286562021C2776214188 @default.
• W4286562021 hasConceptScore W4286562021C2778112365 @default.
• W4286562021 hasConceptScore W4286562021C2910714999 @default.
• W4286562021 hasConceptScore W4286562021C41008148 @default.
• W4286562021 hasConceptScore W4286562021C45484198 @default.
• W4286562021 hasConceptScore W4286562021C54355233 @default.

• next