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Discriminative modelling of context-specific amino acid substitution probabilities

Christof Angermüller, Andreas Biegert, Johannes Söding
2012 Computer applications in the biosciences : CABIOS  
Alignments are assessed using their similarity scores, essentially the sum of substitution matrix scores over all pairs of aligned amino acids.  ...  Results: Here, we develop an alternative discriminative approach to predict sequence context-specific substitution scores.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bts622 pmid:23080114 fatcat:jdwkeassmjcxdjz3cuisw7jzvu

Evidence for Positive Selection on the Floral Scent Gene Isoeugenol-O-methyltransferase

T. J. Barkman
2003 Molecular biology and evolution  
IEMT likely evolved by gene duplication from caffeic acid-O-methyltransferase followed by amino acid divergence, leading to the acquisition of its novel function.  ...  Most of these positions are in the active site of IEMT and have been shown by site-directed mutagenesis to have large effects on substrate specificity.  ...  Acknowledgments Ziheng Yang, DeWayne Shoemaker, and two anonymous reviewers are thanked for comments and suggestions on earlier drafts of this manuscript.  ... 
doi:10.1093/molbev/msg030 pmid:12598682 fatcat:tzqdwzo2erdljbzmvyrvyu2n4a

Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo

Koen Deforche, Ricardo Camacho, Kristel Van Laethem, Beth Shapiro, Yves Moreau, Andrew Rambaut, Anne-Mieke Vandamme, Philippe Lemey
2007 Journal of Computational Biology  
Although dinucleotide context was responsible for variation in misincorporation probabilities, this variation was not specific for G to A mutations implying that the footprint of APOBEC3G/3F editing could  ...  The technique is robust to selection on the amino acid sequence and selection against CpG dinucleotides.  ...  K.D. was funded by a Ph.D grant of the Institute for the Promotion of Innovation through Sciences and Technology in Flanders (IWT). P.L. was supported by a long-term EMBO fellowship.  ... 
doi:10.1089/cmb.2007.0073 pmid:17985990 fatcat:fh2e3li6dfeptgzdjioamgwpke

Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences

Eleazar Eskin, William Stafford Noble, Yoram Singer
2002 Journal of Computational Biology  
The method is an extension of substitution matrix-based probability estimation methods.  ...  The method is applied to estimate amino acid probabilities based on observed counts in an alignment and is shown to perform comparably to previous methods.  ...  This research of YS was partially funded by the Israeli Science Foundation grant 032.9627. Thanks to C. Leslie for useful comments.  ... 
doi:10.1089/10665270260518263 pmid:12614546 fatcat:27emwo2itzcojf6om6yrqnnlza

A Similar Fragments Merging Approach to Learn Automata on Proteins [chapter]

François Coste, Goulven Kerbellec
2005 Lecture Notes in Computer Science  
Quality of the characterization of the major intrinsic protein (MIP) family is assessed by leave-one-out cross-validation for a large range of models specificity.  ...  We propose here to learn automata for the characterization of proteins families to overcome the limitations of the position-specific characterizations classically used in Pattern Discovery.  ...  Substitution matrices, like PAM and BLOSUM, provide the probability (or odds) of changing one amino acid into another.  ... 
doi:10.1007/11564096_50 fatcat:n4zy3naukvax5kq5hcdnw5grcu

Correlated substitution analysis and the prediction of amino acid structural contacts

D. S. Horner, W. Pirovano, G. Pesole
2007 Briefings in Bioinformatics  
It has long been suspected that analysis of correlated amino acid substitutions should uncover pairs or clusters of sites that are spatially proximal in mature protein structures.  ...  We review methods for the detection of correlated amino acid substitutions, compare their relative performance in contact prediction and predict future directions in the field.  ...  Such models typically allow the incorporation of dataset-specific amino acid frequencies [6] and variability in site substitution rates.  ... 
doi:10.1093/bib/bbm052 pmid:18000015 fatcat:frlgf7yqcnhv7kdy2zudr4ib44

Automated inference of molecular mechanisms of disease from amino acid substitutions

B. Li, V. G. Krishnan, M. E. Mort, F. Xin, K. K. Kamati, D. N. Cooper, S. D. Mooney, P. Radivojac
2009 Bioinformatics  
Over the last decade, a number of computational methods have been developed to predict whether such amino acid substitutions result in an altered phenotype.  ...  Single nucleotide substitutions within protein coding regions are of particular importance owing to their potential to give rise to amino acid substitutions that affect protein structure and function which  ...  Funding: National Institutes of Health R01LM009722 to S.D.M. and National Science Foundation DBI-0644017 to P.R. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp528 pmid:19734154 pmcid:PMC3140805 fatcat:46h4jv4sone2rc3qrl3z4yiq5u

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms

S. Balasubramanian
2005 Nucleic Acids Research  
Logistic regression analyses indicated that position-specific phylogenetic features that describe the conservation of an amino acid at a specific site are the best discriminators of disease mutations versus  ...  derived from amino-acid scales, such as volume and hydrophobicity; (2) Position-specific phylogenetic features reflecting evolutionary conservation, such as normalized site entropy, residue frequency  ...  YX is a Fellow of the Jane Coffin Childs Memorial Fund for Medical Research.  ... 
doi:10.1093/nar/gki311 pmid:15784611 pmcid:PMC1069129 fatcat:uxe6vpzmjvg6tavhfkdp7xpm7i

Detecting consistent patterns of directional adaptation using differential selection codon models

Sahar Parto, Nicolas Lartillot
2017 BMC Evolutionary Biology  
The model parameterizes the global mutational pressure, as well as the site-and condition-specific amino acid selective preferences.  ...  Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by explicitly modelling the amino acid fitness landscape along the sequence  ...  Acknowledgement We are thankful to the Natural Sciences and Engineering Research Council of Canada (NSERC) for financially supporting this research.  ... 
doi:10.1186/s12862-017-0979-y pmid:28645318 pmcid:PMC5481935 fatcat:42343ghi3vhkbbmgfhe5rifvyq

Molecular adaptation in Rubisco: discriminating between convergent evolution and positive selection using mechanistic and classical codon models [article]

Sahar Parto, Nicolas Lartillot
2016 bioRxiv   pre-print
However, convergent adaptation is expected to leave a different molecular signature, taking the form of repeated transitions toward identical or similar amino acids.  ...  Molecular adaptation is often identified with positive selection and is typically characterized by an elevated ratio of non-synonymous over synonymous substitution rates (dN/dS).  ...  adaptive amino acid states, thereby stopping the flux of adaptive substitutions at those sites.  ... 
doi:10.1101/073684 fatcat:hvtrjtldcjcplnbr2zvyy2ieaq

Molecular adaptation in Rubisco: Discriminating between convergent evolution and positive selection using mechanistic and classical codon models

Sahar Parto, Nicolas Lartillot, Art F. Y. Poon
2018 PLoS ONE  
However, convergent adaptation is expected to leave a different molecular signature, taking the form of repeated transitions toward identical or similar amino acids. .  ...  We find that the two classes of models tend to select distinct, although overlapping, sets of positions.  ...  adaptive amino acid states, thereby stopping the flux of adaptive substitutions at those sites.  ... 
doi:10.1371/journal.pone.0192697 pmid:29432438 pmcid:PMC5809049 fatcat:hc3joaj6mzdzjggdxeso4b5bau

Learning the Language of Biological Sequences [chapter]

François Coste
2016 Topics in Grammatical Inference  
While some first successes have already been recorded, such as the inference of profile hidden Markov models or stochastic context-free grammars which are now part of the classical bioinformatics toolbox  ...  field, we survey here the main ideas and concepts behind the approaches developed in pattern/motif discovery and grammatical inference to characterize successfully the biological sequences with their specificities  ...  of context-free model.  ... 
doi:10.1007/978-3-662-48395-4_8 fatcat:eojckskf65f5phcbmjsfbq7era

Zinc finger-DNA recognition: analysis of base specificity by site-directed mutagenesis

Jeannette Nardelli, Toby Gibson, Patrick Charnay
1992 Nucleic Acids Research  
However, the specificity of recognition was dramatically modified at the expected bases, in a manner that could be explained by examining the newly introduced amino acids within the context of the overall  ...  Zinc fingers of the Cys2/His2 class are conserved 28 -30 amino acid motifs that constitute an important and widespread family of eukaryotic DNA-binding domains.  ...  It reaffirms that the main determinant of discrimination of the middle base is the amino acid at position 18.  ... 
doi:10.1093/nar/20.16.4137 pmid:1508708 pmcid:PMC334117 fatcat:h2unsnan7jdyvcksolzlek3vqe

Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences

E. Eskin, W. N. Grundy, Y. Singer
2001 Bioinformatics  
The method is an extension of substitution matrix-based probability estimation methods.  ...  The method is applied to estimate amino acid probabilities based on observed counts in an alignment and is shown to perform comparably to previous methods.  ...  Part of his research was funded S72 Mixtures of common ancestors by Israeli Ministry of Science, grant number 489/00-1. Thanks to C. Leslie for useful comments.  ... 
doi:10.1093/bioinformatics/17.suppl_1.s65 pmid:11472994 fatcat:fjdrpv4pfrgh5bix6zn7vw5kji

Different modes of stop codon restriction by the Stylonychia and Paramecium eRF1 translation termination factors

S. Lekomtsev, P. Kolosov, L. Bidou, L. Frolova, J.-P. Rousset, L. Kisselev
2007 Proceedings of the National Academy of Sciences of the United States of America  
Using the site-directed mutagenesis, we show that Paramecium eRF1 specificity toward UGA resides within the NIKS (amino acids 61-64) and YxCxxxF (amino acids 124 -131) motifs.  ...  Using both in vitro and in vivo assays, we show here that chimeric molecules composed of the N-terminal domain of Stylonychia eRF1 fused to the core domain (MC domain) of human eRF1 retained specificity  ...  Molecular modeling of RNA-binding propensities for amino acid residues of ciliate and conventional eRF1s has been undertaken (25) .  ... 
doi:10.1073/pnas.0703887104 pmid:17573528 pmcid:PMC1904165 fatcat:j3d2orpozveibhr6i2tps5scxi
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