Antiviral software systems (AVSs) have problems in identifying polymorphic variants of viruses without explicit signatures for such variants. Alignment-based techniques from bioinformatics may provide a novel way to g...Antiviral software systems (AVSs) have problems in identifying polymorphic variants of viruses without explicit signatures for such variants. Alignment-based techniques from bioinformatics may provide a novel way to generate signatures from consensuses found in polymorphic variant code. We demonstrate how multiple sequence alignment supplemented with gap penalties leads to viral code signatures that generalize successfully to previously known polymorphic variants of JS. Cassandra virus and previously unknown polymorphic variants of W32.CTX/W32.Cholera and W32.Kitti viruses. The implications are that future smart AVSs may be able to generate effective signatures automatically from actual viral code by varying gap penalties to cover for both known and unknown polymorphic variants.展开更多
In this paper, we present parallel programming approaches to calculate the values of the cells in matrix’s scoring used in the Smith-Waterman’s algorithm for sequence alignment. This algorithm, well known in bioinfo...In this paper, we present parallel programming approaches to calculate the values of the cells in matrix’s scoring used in the Smith-Waterman’s algorithm for sequence alignment. This algorithm, well known in bioinformatics for its applications, is unfortunately time-consuming on a serial computer. We use formulation based on anti-diagonals structure of data. This representation focuses on parallelizable parts of the algorithm without changing the initial formulation of the algorithm. Approaching data in that way give us a formulation more flexible. To examine this approach, we encode it in OpenMP and Cuda C. The performance obtained shows the interest of our paper.展开更多
This article shows genomic alignment methods using the classic“Needleman”and“Smith-Waterman”algorithms,the latter they were optimized by the ABC(artificial bee colony)algorithm.In the genomic alignment,a goal stat...This article shows genomic alignment methods using the classic“Needleman”and“Smith-Waterman”algorithms,the latter they were optimized by the ABC(artificial bee colony)algorithm.In the genomic alignment,a goal state is not presented,the experiments that are carried out show alternative alignments by ABC were proposed.Different types of alignments could exist within the classical algorithm,based on a horizontal,vertical,diagonal and inverse search mechanism on a match value table.Our ABC-Smith Waterman algorithm was generated from the genomic sequences written in rows and columns for the search for similarities that will provide values that ABC uses to process and provide more results of alignments that can be used by scientists for their experiments and research.展开更多
文摘Antiviral software systems (AVSs) have problems in identifying polymorphic variants of viruses without explicit signatures for such variants. Alignment-based techniques from bioinformatics may provide a novel way to generate signatures from consensuses found in polymorphic variant code. We demonstrate how multiple sequence alignment supplemented with gap penalties leads to viral code signatures that generalize successfully to previously known polymorphic variants of JS. Cassandra virus and previously unknown polymorphic variants of W32.CTX/W32.Cholera and W32.Kitti viruses. The implications are that future smart AVSs may be able to generate effective signatures automatically from actual viral code by varying gap penalties to cover for both known and unknown polymorphic variants.
文摘In this paper, we present parallel programming approaches to calculate the values of the cells in matrix’s scoring used in the Smith-Waterman’s algorithm for sequence alignment. This algorithm, well known in bioinformatics for its applications, is unfortunately time-consuming on a serial computer. We use formulation based on anti-diagonals structure of data. This representation focuses on parallelizable parts of the algorithm without changing the initial formulation of the algorithm. Approaching data in that way give us a formulation more flexible. To examine this approach, we encode it in OpenMP and Cuda C. The performance obtained shows the interest of our paper.
文摘This article shows genomic alignment methods using the classic“Needleman”and“Smith-Waterman”algorithms,the latter they were optimized by the ABC(artificial bee colony)algorithm.In the genomic alignment,a goal state is not presented,the experiments that are carried out show alternative alignments by ABC were proposed.Different types of alignments could exist within the classical algorithm,based on a horizontal,vertical,diagonal and inverse search mechanism on a match value table.Our ABC-Smith Waterman algorithm was generated from the genomic sequences written in rows and columns for the search for similarities that will provide values that ABC uses to process and provide more results of alignments that can be used by scientists for their experiments and research.
