Sequence alignment of CTLDs with solved structure
Prediction Of Antimicrobial Peptides Based On Sequence Alignment And Secondary Structure Sequence And Segment Sequence.pdf
... secondary structure sequence from the prediction of ...including sequence alignment stage and feature extraction process until classification stage is carried out in Perl programming language ...
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iPBA: a tool for protein structure comparison using sequence alignment strategies.: Structural Alphabet Alignment
... accurate structure com- parison has been ...for structure comparison, based on a struc- tural ...3D structure can be translated into a 1D sequence of ...improved alignment approach ...
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Sequence and structure alignment of paramyxovirus hemagglutinin-neuraminidase with influenza virus neuraminidase.
... Site- directed mutagenesis of the neuraminidase active site sug- gests that the enzyme activity is very sensitive to single amino acid sequence changes in both the functional and framewo[r] ...
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An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment
... We want to show that our model yields on aver- age comparable or better alignments than other state- of-the-art programs that build upon more costly dy- namic programming algorithms. We do believe that this comparison is ...
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An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment
... We want to show that our model yields on aver- age comparable or better alignments than other state- of-the-art programs that build upon more costly dy- namic programming algorithms. We do believe that this comparison is ...
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Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization
... Comparison of running times. We compared the programs tested on the same computing server with an Intel Xeon CPU running at 3.2 GHz, 3.5 GB RAM, and Linux kernel version 2.6.16. It turned out that memory requirement was ...
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Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization
... the structure they are forming, because their evolutionary behavior fol- lows the structure-function paradigm: RNA molecules with different sequences but same or similar secondary struc- ture are likely to ...
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An enhanced RNA alignment benchmark for sequence alignment programs
... Most sequence alignment programs perform equally well on RNA sequence sets with high sequence identity, that is with an average pairwise sequence identity (APSI) above 75 ...on ...
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An enhanced RNA alignment benchmark for sequence alignment programs
... Most sequence alignment programs perform equally well on RNA sequence sets with high sequence identity, that is with an average pairwise sequence identity (APSI) above 75 ...on ...
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CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments
... involving structure-based comparison of Reston Ebolavirus sGP with the corresponding proteins from several other Ebolavirus species ...combining structure-based alignments can reveal structural (and ...
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Sequence and structure alignment of Paramyxoviridae attachment proteins and discovery of enzymatic activity for a morbillivirus hemagglutinin.
... multiple sequence alignment of paramyxovirus HN proteins was used as an intermediate to align the morbillivirus hemagglutinin (H) proteins with ...3D structure of HN and H of the ...
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Improved computational methods of protein sequence alignment, model selection and tertiary structure prediction
... query-template alignment, the percent of identical residue pairs in aligned positions, the percent of residues of the query that are aligned with a residue in the template, and the average of BLOSUM [93] scores of ...
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Robust and Efficient Algorithms for Protein 3-D Structure Alignment and Genome Sequence Comparison
... and structure analysis are two of the fundamental areas of bioinfor- matics ...protein structure related problems including protein structure alignment and query, and genome sequence ...
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Bayesian coestimation of phylogeny and sequence alignment
... linear-time algorithm that computes the likelihood of observing a set of sequences and their homology struc- ture, given a phylogeny and evolutionary parameters, under the TKF91 model [31]. By definition, this likeli- ...
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Heuristics for multiobjective multiple sequence alignment
... of sequence alignment provides the practitioner a set of alignments that represents the trade-off between decreasing the number of gaps and increasing ...pairwise sequence (DNA/Protein) ...
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Improving the quality of multiple sequence alignment
... secondary structure predictions into the pair-HMM model as follows: in state M, we introduce an additional parameter α and subdivide the emission probability e’(i, j) into two cases to obtain a modified state M( α ...
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Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure
... the sequence using evolutionary information in the form of multiple sequence ...multiple- sequence alignment obtained from PSI-BLAST is used as input instead of a single ...a ...
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Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... secondary structure [6], but which can be used for protein se- quence ...first sequence alignment viewer and editor implemented in Java, a platform independent programming language allowing graphical ...
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Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... multiple sequence alignments (MSAs) is a fundamental requirement in the analysis of protein sequences, allowing us to visu- alize conservation across protein families as well as unusual features of particular ...
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A Novel Approach to Structure Alignment
... One approach within the first category is the iterative dynamical programming method [?, ?], where one first computes a distance matrix between all pairs of atoms (e.g. C α ) forming a similarity matrix, which by ...
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