Multiple sequence alignment in parallel on a workstation cluster

Multiple sequence alignment in parallel on a workstation cluster

SUMMARY Multiple sequence alignment is the NP-hard problem of aligning three or more DNA or amino acid sequences in an optimal way so as to match as many characters as possible from the set of sequences. The popular sequence alignment program ClustalW uses the classical method of approximating a sequence alignment, by first computing a distance matrix and then constructing a guide tree to show ...

Parallel FSA: Improving the Performance of Multiple Sequence Alignment using a Workstation Cluster and Database

Multiple Sequence Alignments (MSA) are widely-used tools for biological sequence analysis such as function prediction and phylogeny inference. Recently, a MSA algorithm based on a statistically-sound method for model selection and parameterization, Fast Statistical Alignment (FSA), has been introduced. Although FSA is state-of-the-art with respect to accuracy and ability to scale to thousands o...

DNA sequence alignment: hybrid parallel programming on a multicore cluster

DNA sequence alignment is one of the most important operations of computational biology. In 1981, Smith and Waterman developed a method for sequences local alignment. Due to its computational power and memory requirements, various heuristics have been developed to reduce execution time at the expense of a loss of accuracy in the result. This is why heuristics do not ensure that the best alignme...

Parallel Workstation Cluster for Algorithm

Cluster Analysis Method for Multiple Sequence Alignment

With the addition of more data in the field of proteomics, the computational methods need to be more efficient. The fraction or the part of molecular sequence that is more resistant to change is functionally more important to the molecule. Comparative approaches are used to ensure the reliability of sequence alignment. The problem of multiple sequence alignment (MSA) is a proposition of evoluti...