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2016
The increasing importance of Next Generation Sequencing (NGS) techniques has highlighted the key role of multiple sequence alignment (MSA) in comparative structure and function analysis of biological sequences. MSA often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families ...
Bawono, Punto +5 more
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The increasing importance of Next Generation Sequencing (NGS) techniques has highlighted the key role of multiple sequence alignment (MSA) in comparative structure and function analysis of biological sequences. MSA often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families ...
Bawono, Punto +5 more
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An Overview of Multiple Sequence Alignment
Current Protocols in Bioinformatics, 2003AbstractMultiple sequence alignment is perhaps the most commonly applied bioinformatics technique. It often leads to fundamental biological insight into sequence‐structure‐function relationships of nucleotide or protein sequence families. In this unit, an overview of multiple sequence alignment techniques is presented, covering a history of nearly 30 ...
Victor, Simossis +2 more
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Multiple Sequence Alignment on an FPGA
11th International Conference on Parallel and Distributed Systems (ICPADS'05), 2006Molecular biologists frequently compute multiple sequence alignments (MSAs) to identify similar regions in protein families. Progressive alignment is a widely used approach to compute MSAs. However, aligning a few hundred sequences by popular progressive alignment tools requires several hours on sequential computers.
Timothy F. Oliver +4 more
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Multithreaded Multiple Sequence Alignments
2005 IEEE Engineering in Medicine and Biology 27th Annual Conference, 2005Based on the mixed idea of Progressive alignment and Divide-and-conquer alignment, two different multithreaded multiple sequence alignment programs, depending on how the guide tree(s) would be applied, are implemented for checking the improvements of alignment speed and sensitivity.
Joanne, Bai, Siamak, Rezaei
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Multiple protein sequence alignment
Current Opinion in Structural Biology, 2008Multiple sequence alignments are essential in computational analysis of protein sequences and structures, with applications in structure modeling, functional site prediction, phylogenetic analysis and sequence database searching. Constructing accurate multiple alignments for divergent protein sequences remains a difficult computational task, and ...
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Overestimation for Multiple Sequence Alignment
2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, 2007Multiple sequence alignment is an important problem in computational biology. A-star is an algorithm that can be used to find exact alignments. We present a simple modification of the A-star algorithm that improves much multiple sequence alignment, both in time and memory, at the cost of a small accuracy loss.
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Aligning Multiple RNA Sequences
1991Each cell in a living organism contains a complete design for all of the mechanisms that sustain its life. This blueprint is encoded in DNA and is called the genome of the organism. The basic activity of the cell involves maintaining an environment in which appropriate concentrations of specific proteins drive the reactions that characterize its normal
Ross A. Overbeek, Ian T. Foster
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DNA multiple sequence alignments
2002In this chapter we examine the procedure of multiple sequence alignment. We first examine the heuristic procedures commonly used in multiple sequence alignment. Next we examine sources of ambiguity involved in the alignment procedure. We suggest that several alignment parameters be employed to examine alignment sensitivity.
Gonzalo, Giribet +2 more
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Optimization of multiple‐sequence alignment based on multiple‐structure alignment
Proteins: Structure, Function, and Bioinformatics, 2005AbstractRoutinely used multiple‐sequence alignment methods use only sequence information. Consequently, they may produce inaccurate alignments. Multiple‐structure alignment methods, on the other hand, optimize structural alignment by ignoring sequence information.
Maxim, Shatsky +2 more
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Assessing the Discordance of Multiple Sequence Alignments
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009Multiple sequence alignments have wide applicability in many areas of computational biology, including comparative genomics, functional annotation of proteins, gene finding, and modeling evolutionary processes. Because of the computational difficulty of multiple sequence alignment and the availability of numerous tools, it is critical to be able to ...
Amol Prakash, Martin Tompa
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