Results 1 - 10 of 64

Protein homology detection by HMM-HMM comparison

by Johannes Söding - BIOINFORMATICS , 2005
"... Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction, and evolution. Results: We have generalized the alignment of protein se-quences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile H ..."
Abstract - Cited by 401 (8 self) - Add to MetaCart
Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction, and evolution. Results: We have generalized the alignment of protein se-quences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile

Contextual Multiple Sequence Alignment

by Anna Gambin , Rafał Otto
"... In a recently proposed contextual alignment model, efficient algorithms exist for global and local pairwise alignment of protein sequences. Preliminary results obtained for biological data are very promising. Our main motivation was to adopt the idea of context dependency to the multiple alignment ..."
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In a recently proposed contextual alignment model, efficient algorithms exist for global and local pairwise alignment of protein sequences. Preliminary results obtained for biological data are very promising. Our main motivation was to adopt the idea of context dependency to the multiple alignment

Archive of SID gpALIGNER: A Fast Algorithm for Global Pairwise Alignment of DNA Sequences

by Hadian Dehkordi, Mostafa Masoudi-nejad, Mohamad-mouri Morteza
"... ABSTRACT: Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the sequence alignment problem. Dynamic pro ..."
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ABSTRACT: Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the sequence alignment problem. Dynamic

Global alignment of pairwise protein interaction networks for maximal common conserved patterns

by Wenhong Tian , Nagiza F Samatova - Int. J. Genomics , 2013
"... A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researcher ..."
Abstract - Cited by 2 (0 self) - Add to MetaCart
A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences

Simultaneous Alignment and Folding of Protein Sequences

by Jérôme Waldispühl, Charles W. O’donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
"... Abstract. Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned ..."
Abstract - Cited by 1 (0 self) - Add to MetaCart
protein sequences; the algorithm’s complexity is polynomial in time and space. Algorithmically, partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We

BMC Bioinformatics BioMed Central Methodology article Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

by Robin D Dowell, Sean R Eddy Open Access, Robin D Dowell, Sean R Eddy , 2006
"... which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into ..."
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assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. Conclusion: Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding

Learning to align: a statistical approach

by Elisa Ricci, Tijl De Bie, Nello Cristianini
"... Abstract. We present a new machine learning approach to the inverse parametric sequence alignment problem: given as training examples a set of correct pairwise global alignments, find the parameter values that make these alignments optimal. We consider the distribution of the scores of all incorrect ..."
Abstract - Cited by 3 (1 self) - Add to MetaCart
Abstract. We present a new machine learning approach to the inverse parametric sequence alignment problem: given as training examples a set of correct pairwise global alignments, find the parameter values that make these alignments optimal. We consider the distribution of the scores of all

A hidden Markov model for progressive multiple alignment

by Ari Löytynoja, Michel C. Milinkovitch - Bioinformatics , 2003
"... Motivation: Progressive algorithms are widely used heuristics for the production of alignments among multiple nucleic-acid or protein sequences. Probabilistic approaches providing measures of global and/or local reliability of individual solutions would constitute valuable developments. Results: We ..."
Abstract - Cited by 48 (2 self) - Add to MetaCart
Motivation: Progressive algorithms are widely used heuristics for the production of alignments among multiple nucleic-acid or protein sequences. Probabilistic approaches providing measures of global and/or local reliability of individual solutions would constitute valuable developments. Results: We

Research Articles Simultaneous Alignment and Folding of Protein Sequences

by Rolf Backofen, Bonnie Berger
"... Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein se ..."
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sequences; the algorithm’s complexity is polynomial in time and space. Algorithmically, partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate

Research Article Simultaneous Alignment and Folding of Protein Sequences

by Jérôme Waldispühl, Charles W. O’donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
"... Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein se ..."
Abstract - Add to MetaCart
sequences; the algorithm’s complexity is polynomial in time and space. Algorithmically, partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate
Results 1 - 10 of 64