Pairwise Alignment, Multiple Alignment, and BLAST

2018 ◽  
pp. 51-79
Author(s):  
Henrik Christensen ◽  
John Elmerdahl Olsen
Keyword(s):  
Pairwise Alignment ◽  
Multiple Alignment

scholarly journals Contextual Multiple Sequence Alignment

2005 ◽  
Vol 2005 (2) ◽  
pp. 124-131 ◽  
Author(s):  
Anna Gambin ◽  
Rafał Otto
Keyword(s):  
Pairwise Alignment ◽  
Multiple Alignment ◽  
Biological Data ◽  
Context Dependency ◽  
Alignment Algorithm ◽  
Orphan Genes ◽  
Multiple Sequence ◽  
New Family ◽  
Substitution Matrices ◽  
Global And Local

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 setting. To this aim the relaxation of the model was developed (we call this new modelaveraged contextual alignment) and a new family of amino acids substitution matrices are constructed. In this paper we present a contextual multiple-alignment algorithm and report the outcomes of experiments performed for the BAliBASE test set. The contextual approach turned out to give much better results for the set of sequences containing orphan genes.

A Heuristic Method Based on Multi-Objective Optimization Concept for Solving RNA Multiple Alignment

2017 ◽  
Vol 10 (5) ◽  
pp. 371
Author(s):  
Arakil Chentoufi ◽  
Abdelhakim El Fatmi ◽  
Molay Ali Bekri ◽  
Said Benhlima ◽  
Mohamed Sabbane
Keyword(s):  
Heuristic Method ◽  
Multiple Alignment ◽  
Multi Objective Optimization ◽  
Multi Objective

scholarly journals PRALINETM: a strategy for improved multiple alignment of transmembrane proteins

2008 ◽  
Vol 24 (4) ◽  
pp. 492-497 ◽  
Author(s):  
W. Pirovano ◽  
K. A. Feenstra ◽  
J. Heringa
Keyword(s):  
Transmembrane Proteins ◽  
Multiple Alignment

scholarly journals BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs

1999 ◽  
Vol 15 (1) ◽  
pp. 87-88 ◽  
Author(s):  
J. Thompson ◽  
F Plewniak ◽  
O Poch
Keyword(s):  
Multiple Alignment

scholarly journals An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees

2003 ◽  
Vol 10 (6) ◽  
pp. 869-889 ◽  
Author(s):  
G. A. Lunter ◽  
I. Miklós ◽  
Y. S. Song ◽  
J. Hein
Keyword(s):  
Efficient Algorithm ◽  
Phylogenetic Trees ◽  
Multiple Alignment
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