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64
Protein homology detection by HMM-HMM comparison
- 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
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Cited by 401 (8 self)
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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
"... 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
"... 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
- 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
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Cited by 2 (0 self)
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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
"... 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 ..."
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Cited by 1 (0 self)
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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
, 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
"... 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
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Cited by 3 (1 self)
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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
- 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
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Cited by 48 (2 self)
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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
"... 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
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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
"... 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
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64