Multiple sequence alignment and Similarity plot
Heuristics for multiobjective multiple sequence alignment
... We analysed the effect of different k-values in the k-block neighborhood, as well as the effect of the three starting alignments on the performance of PLS. For a given instance, let Min denote the length of the smallest ...
17
Improving the quality of multiple sequence alignment
... the multiple alignment problem is to bring similar regions from different sequences as closely together as possible, with applications in diverse types of biosequence analysis (Taylor, 1987; Carillo and ...
120
INTERPLAY BETWEEN MULTIPLE ALIGNMENT AND STRUCTURAL ANALYSIS OF PROTEINS: SEQUENCE VERSUS STRUCTURE SIMILARITY. (SHORT REVIEW)
... and sequence versus structure similarity. A protein sequence is an important piece of information , it becomes more revealing and valuable when compared with others from a variety of different ...
5
A Tabu Search Approach to Multiple Sequence Alignment
... regional similarity. Gapped BLAST attempts to opti- mize a similarity measure by searching the database in two ...of similarity with sequence ...
114
Multiple Sequence Alignment by Conformational Space Annealing
... for multiple sequence alignment (MSA), which we call ...pairwise sequence alignments between constituting ...recent alignment method ...minimum alignment but also many distinct ...
7
Progressive Multiple Sequence Alignment with Indel Evolution
... While changes between homologous characters are typically modeled by a Markov substitution process, the dynamics of indels, with a few notable exceptions, is never modeled explicitly. The reason lies in the fact that the ...
267
Cluster Analysis Method for Multiple Sequence Alignment
... the alignment of lengthy, highly variable or extremely numerous sequences that cannot be aligned solely by human ...high-quality sequence alignments, and occasionally in adjusting the final results to ...
7
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- ...
10
MSARC: Multiple sequence alignment by residue clustering
... Fiduccia-Mattheyses algorithm needs to be modified in order to deal with alignment graphs. Mainly, residues are not moved independently; since the graph topology has to be maintained, moving a residue involves ...
11
Assessing the efficiency of multiple sequence alignment programs
... See Additional file 3 and Additional file 4 for more de- tailed comparisons. Discussion Many MSA programs are freely available. However, choosing the most suitable program to each dataset is not trivial. The ...
8
Progressive multiple sequence alignment with indel evolution
... the alignment of two MSAs by ML, which exploits PIP’s linear time complexity for the computation of marginal likeli- ...particular alignment length) depend only on the layer above (and not on each ...
8
Memory-Efficient A* Heuristics for Multiple Sequence Alignment
... In multiple sequence alignment, three or more se- quences must be aligned, so even with Hirschberg-style one- dimensional space reductions, DP algorithms still require too much ...the ...
7
Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... a sequence and the se- quence itself — all sequences must be ...of alignment col- umn positions to be highlighted; (ii) the colour scheme to be used; (iii) whether the sequence should be doti- fied ...
6
Sequence embedding for fast construction of guide trees for multiple sequence alignment
... The trees from mBed are generated strictly by grouping similar sequences rather than by attempting to accurately reconstruct phylogenetic branching orders. This would make us advise against using mBed directly for large ...
11
Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... Viewing 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 ...
10
Multiple Sequence Alignment and Analysis: Part I An Introduction to the Theory and Application of Multiple Sequence Analysis.
... database similarity searching can be very helpful for sorting any collection of GCG sequence specifications into order of alignment ...a sequence database, but rather, on the results of ...
53
Protein sequence alignment with family specific amino acid similarity matrices
... improve sequence alignment of structurally-simi- lar proteins from the “twilight ...in alignment quality score and the average sequence identity in both SUP and TWI ...
10
Bootstrapping Lexical Choice via Multiple Sequence Alignment
... applies multiple-sequence alignment techniques to the mapping-dictionary acquisition ...of multiple verbalizations helps the system learn several ways to express ...
8
Prenominal Modifier Ordering via Multiple Sequence Alignment
... To overcome this issue, Shaw and Hatzi- vassiloglou’s transitivity and clustering meth- ods make inferences about unseen orderings among prenominal modifiers. In the transitiv- ity method, given three modifiers a,b,c, ...
9
Improving and extending the multiple sequence alignment suite PRALINE
... The scoring function should ideally incorporate information about all sequence features as soft constraints. We have already introduced simplest forms of scoring – a penalty for a mismatch or a gap and a bonus for ...
73