protein sequence alignment
FPGA-based protein sequence alignment : A review
... of protein sequence alignment can be done with some modification to the SW algorithm with used the only one row version of an alignment matrix named ‘one row c’ as reference for the next ...
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Fragmented protein sequence alignment using two-layer particle swarm optimization (FTLPSO)
... Fragmented protein sequence alignment using two-layer PSO (FTLPSO) method to overcome the drawbacks of particle swarm optimization (PSO) and improve its performance in solving multiple ...
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Protein sequence alignment with family specific amino acid similarity matrices
... matrix-based alignment, matrix selec- tion is the most important decision the user has to make because once a matrix is selected the values of its elements cannot be easily changed, unlike gap ...equivalent ...
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Applying Hidden Markov Model to Protein Sequence Alignment
... Sequence alignment is a way of writing one sequence on top of another where the residues in one position are supposed to have a common evolutionary ...other sequence to signify such an ...
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A Deep Ensemble Model with Slot Alignment for Sequence to Sequence Natural Language Generation
... NLG is closely related to machine translation and has similarly benefited from recent rapid develop- ment of deep learning methods. State-of-the-art NLG systems build thus on deep neural sequence- ...
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Progressive Multiple Sequence Alignment with Indel Evolution
... an alignment, nevertheless manual curated alignments are highly subject to personal judge- ment which lack of standard rules and therefore not replicable ...entire alignment space to select the most ...
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A novel genetic approach for optimized biological sequence alignment
... Bioinformatics, sequence alignment is a crucial technique for obtaining matching pattern between a known and an unknown ...or protein sequences to detect and quantify the similarities between two ...
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BioBCDM: A novel integrated tool in Sequence alignment
... Bioinformatics is a rapid processing field. Both the experimental technologies and the computer based methods are in dynamic phase of development. While some years ago human experts would check every program output, ...
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Prenominal Modifier Ordering via Multiple Sequence Alignment
... from alignment of biolog- ical sequences in that we have little prior knowl- edge of the similarity between ...choosing alignment order (i.e., which sequence to align next) and during the actual ...
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Assessing the efficiency of multiple sequence alignment programs
... The efficiency of MSA programs can benchmarked, resulting in useful guidelines. In order to assess and compare the efficiency of the nine programs listed above, the BAliBASE benchmark dataset was selected [16]. BAliBASE ...
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MSARC: Multiple sequence alignment by residue clustering
... progressive alignment is usually preceded by consis- tency transformation (incorporating information from all pairwise alignments into the objective function) and/or followed by iterative refinement of the ...
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Cluster Analysis Method for Multiple Sequence Alignment
... individual sequence regions, is qualitative and simple, though time-consuming to analyze on a large ...certain sequence features—such as insertions, deletions, repeats, or inverted repeats—from a dot-matrix ...
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Instability in progressive multiple sequence alignment algorithms
... real alignment scores using an amino acid weight matrix such as BLOSUM [7], the number of possible scores is still finite although much greater than with k-tuple ...such alignment scores is limited how- ...
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A Complete and Accurate Short Sequence Alignment Algorithm for Repeats
... Genome repeats of eukaryotes occupy a significant fraction of the eukaryotes genomes. Most of them have played and are continuing to play critical roles in genome evolution. In order to align these repeats more ...
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Alignment free sequence comparison: benefits, applications, and tools
... a sequence alignment depends on multiple a priori assumptions about the evolution of the sequences that are being ...choose alignment parameters may often cause problems and usually requires a trial ...
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Detection of Android Malware based on Sequence Alignment of Permissions
... There are two datasets: malicious samples and normal samples (line 1). The sequence alignment between its DNA and the DNA of the whole malware is applied for every malicious and normal sample A (lines 3.b ...
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Multiple sequence alignment with user-defined anchor points
... automated alignment procedures can produce biologically incorrect ...primary sequence level may be obscured by spurious random ...for alignment programs are duplications within the input ...by ...
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Modular and configurable optimal sequence alignment software: Cola
... the alignment can no longer be performed in two dimensions, Cola implements a three-dimensional graph structure analogous to the 'edit-graph' used by SW and ...query sequence is represented horizontally and ...
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Alignment-free sequence comparison with spaced k-mers
... biological sequence comparison, see for example ...Fast alignment programs such as FASTA [27] and BLAST [1] originally relied on identifying word matches of a fixed ...local alignment step is the ...
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A Modified Dynamic Parallel Algorithm for Sequence Alignment in BioSequences
... optimal alignment of x[1..i] and y[1..j] , where an alignment is defined to be the path from the top-left corner to the bottom-right corner of the Needleman-Wunsch ...
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