A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Filters
Discriminative modelling of context-specific amino acid substitution probabilities
2012
Computer applications in the biosciences : CABIOS
Preserved Fulltext
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
2003
Molecular biology and evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2007
Journal of Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2002
Journal of Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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]
2005
Lecture Notes in Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2007
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2009
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2009; you can also visit the original URL.
The file type is application/pdf.
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
2005
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2005; you can also visit the original URL.
The file type is application/pdf.
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
2017
BMC Evolutionary Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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]
2016
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2018
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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]
2016
Topics in Grammatical Inference
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
1992
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2001
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2007
Proceedings of the National Academy of Sciences of the United States of America
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 18,111 results