caa a22 4500 44582154X CHVBK 20180317145245.0 cr unu---uuuuu 170323e20110201xx s 000 0 eng 10.1007/s00239-010-9409-0 doi (NATIONALLICENCE)springer-10.1007/s00239-010-9409-0 Regional Context in the Alignment of Biological Sequence Pairs [Elektronische Daten] [Raymond Sammut, Gavin Huttley] Sequence divergence derives from either point substitution or indel (insertion or deletion) processes. We investigated the rates of these two processes both in protein and non-protein coding DNA. We aligned sequence pairs using two pair-hidden Markov models (PHMMs) conjoined by one silent state. The two PHMMs had their own set of parameters to model rates in their respective regions. The aim was to test the hypothesis that the indel mutation rate mimics the point mutation rate. That is, indels are found less often in conserved regions (slow point substitution rate) and more often in non-conserved regions (fast point substitution rate). Both polypeptides and rRNA molecules in our data exhibited a clear distinction between slow and fast rates of the two processes. These two rates served as surrogates to conserved and non-conserved secondary structure components, respectively. With polypeptides we found both the fast indel rate and the fast replacement rate were co-located with hydrophilic residues. We also found that the average concordance, of our alignments with corresponding curated alignments, improves markedly when the model allows either of the two fast rates to colocate with hydrophilic residues. With rRNA molecules, our model did not detect colocation between the fast indel rate and the fast substitution rate. Nevertheless, coupling the indel rates with the point substitution rates across the two regions markedly increased model fit. This result suggests that rRNA pairwise alignments should be modeled after allowing for the two processes to vary simultaneously and independently in the two regions. The Author(s), 2010 Indel nationallicence Polypeptide nationallicence rRNA nationallicence Pairwise alignment nationallicence PHMM nationallicence Colocation nationallicence Concordance nationallicence Hydrophilic residue nationallicence rRNA : Ribosomal RNA nationallicence HMM : Hidden Markov model nationallicence PHMM : Pair-hidden Markov model nationallicence PIP : Phylogenetically independent sequence pair nationallicence PMB : Probability matrix from blocks nationallicence Replacement : The change of one amino acid in one sequence to another amino acid in the other sequence at a site of a pairwise alignment of two biological sequences nationallicence N/C-terminal : The N-terminus is the start of the polypeptide terminated by an amino acid with a free amine group (-NH2), and the C-terminus is the end of a polypeptide terminated by an amino acid with a free carboxyl group (-COOH), by convention, a peptide sequence is written from N-terminus on the left hand side to the C-terminus on the right nationallicence Sammut Raymond Department of Genome Biology, John Curtin School of Medical Research, Building 54, The Australian National University, 0200, Canberra, ACT, Australia aut Huttley Gavin Department of Genome Biology, John Curtin School of Medical Research, Building 54, The Australian National University, 0200, Canberra, ACT, Australia aut Journal of Molecular Evolution Springer-Verlag 72/2(2011-02-01), 147-159 0022-2844 72:2<147 2011 72 239 https://doi.org/10.1007/s00239-010-9409-0 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s00239-010-9409-0 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Sammut Raymond Department of Genome Biology, John Curtin School of Medical Research, Building 54, The Australian National University, 0200, Canberra, ACT, Australia aut NATIONALLICENCE 700 1- Huttley Gavin Department of Genome Biology, John Curtin School of Medical Research, Building 54, The Australian National University, 0200, Canberra, ACT, Australia aut NATIONALLICENCE 773 0- Journal of Molecular Evolution Springer-Verlag 72/2(2011-02-01), 147-159 0022-2844 72:2<147 2011 72 239 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer