scholarly journals A Comparative Analysis of Progressive Multiple Sequence Alignment Approaches using UPGMA and Neighbor Join Based Guide Trees

2015 ◽  
Vol 5 (3/4) ◽  
pp. 1-9 ◽  
Author(s):  
Dega Ravi Kumar Yadav ◽  
Gunes Ercal
Keyword(s):  
Comparative Analysis ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Neighbor Join ◽  
Multiple Sequence ◽  
Progressive Multiple Sequence Alignment ◽  
Guide Trees

scholarly journals NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes

2006 ◽  
Vol 34 (Web Server) ◽  
pp. W394-W399 ◽  
Author(s):  
T. Z. DeSantis ◽  
P. Hugenholtz ◽  
K. Keller ◽  
E. L. Brodie ◽  
N. Larsen ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
16S Rrna ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Multiple Sequence

scholarly journals Progressive multiple sequence alignment with indel evolution

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Massimo Maiolo ◽  
Xiaolei Zhang ◽  
Manuel Gil ◽  
Maria Anisimova
Keyword(s):  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Multiple Sequence ◽  
Progressive Multiple Sequence Alignment

scholarly journals Parallelization of Pairwise Alignment and Neighbor-Joining Algorithm in Progressive Multiple Sequence Alignment

2018 ◽  
Vol 9 (1) ◽  
pp. 234
Author(s):  
Agung Widyo Utomo
Keyword(s):  
Shared Memory ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Programming Model ◽  
Heuristic Method ◽  
Pairwise Alignment ◽  
Neighbor Joining ◽  
Progressive Alignment ◽  
Multiple Sequence ◽  
Progressive Multiple Sequence Alignment

Progressive multiple sequence alignment ClustalW is a widely used heuristic method for computing multiple sequence alignment (MSA). It has three stages: distance matrix computation using pairwise alignment, guide tree reconstruction using neighbor-joining and progressive alignment. To accelerate computing for large data, the progressive MSA algorithm needs to be parallelized. This research aims to identify, decompose and implement the pairwise alignment and neighbor-joining in progressive MSA using message passing, shared memory and hybrid programming model in the computer cluster. The experimental results obtained shared memory programming model as the best scenario implementation with speed up up to 12 times.

scholarly journals Improving multiple sequence alignment by using better guide trees

2015 ◽  
Vol 16 (Suppl 5) ◽  
pp. S4 ◽  
Author(s):  
Qing Zhan ◽  
Yongtao Ye ◽  
Tak-Wah Lam ◽  
Siu-Ming Yiu ◽  
Yadong Wang ◽  
...  
Keyword(s):  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Multiple Sequence ◽  
Guide Trees

scholarly journals Sequence embedding for fast construction of guide trees for multiple sequence alignment

2010 ◽  
Vol 5 (1) ◽  
pp. 21 ◽  
Author(s):  
Gordon Blackshields ◽  
Fabian Sievers ◽  
Weifeng Shi ◽  
Andreas Wilm ◽  
Desmond G Higgins
Keyword(s):  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Multiple Sequence ◽  
Guide Trees
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