A new approach for tree alignment based on local re-optimization

Feng Yue, Jijun Tang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

Multiple sequence alignment is the most fundamental task in bioinformatics and computational biology. In this paper, we present a new algorithm to conduct multiple sequences alignment based on phylogenetic trees. It is widely accepted that a good phylogenetic tree can help produce high quality alignment, but the direct dynamic programming solution grows exponentially [13]. To overcome this problem, we first devise a procedure that can produce optimal alignment for three sequences and infer their common ancestor. We then extend the above procedure to compute the alignment of a given tree with more sequences by iteratively relabeling the internal nodes. We have implemented our algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM or BLOSUM series. We test our new method with biological and simulated datasets, and compare its performance with those of other popular multiple sequence alignment tools, including the widely used programs such as Clustalw and T-Coffee.

Original languageEnglish (US)
Title of host publicationBioMedical Engineering and Informatics
Subtitle of host publicationNew Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008
Pages34-38
Number of pages5
DOIs
StatePublished - Sep 17 2008
EventBioMedical Engineering and Informatics: New Development and the Future - 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008 - Sanya, Hainan, China
Duration: May 27 2008May 30 2008

Publication series

NameBioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008
Volume1

Other

OtherBioMedical Engineering and Informatics: New Development and the Future - 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008
CountryChina
CitySanya, Hainan
Period5/27/085/30/08

Fingerprint

Coffee
Pulse amplitude modulation
Bioinformatics
Dynamic programming
DNA
Substitution reactions
Proteins
Costs

All Science Journal Classification (ASJC) codes

  • Information Systems
  • Signal Processing
  • Biomedical Engineering

Cite this

Yue, F., & Tang, J. (2008). A new approach for tree alignment based on local re-optimization. In BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008 (pp. 34-38). [4548631] (BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008; Vol. 1). https://doi.org/10.1109/BMEI.2008.290
Yue, Feng ; Tang, Jijun. / A new approach for tree alignment based on local re-optimization. BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008. 2008. pp. 34-38 (BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008).
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abstract = "Multiple sequence alignment is the most fundamental task in bioinformatics and computational biology. In this paper, we present a new algorithm to conduct multiple sequences alignment based on phylogenetic trees. It is widely accepted that a good phylogenetic tree can help produce high quality alignment, but the direct dynamic programming solution grows exponentially [13]. To overcome this problem, we first devise a procedure that can produce optimal alignment for three sequences and infer their common ancestor. We then extend the above procedure to compute the alignment of a given tree with more sequences by iteratively relabeling the internal nodes. We have implemented our algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM or BLOSUM series. We test our new method with biological and simulated datasets, and compare its performance with those of other popular multiple sequence alignment tools, including the widely used programs such as Clustalw and T-Coffee.",
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Yue, F & Tang, J 2008, A new approach for tree alignment based on local re-optimization. in BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008., 4548631, BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008, vol. 1, pp. 34-38, BioMedical Engineering and Informatics: New Development and the Future - 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008, Sanya, Hainan, China, 5/27/08. https://doi.org/10.1109/BMEI.2008.290

A new approach for tree alignment based on local re-optimization. / Yue, Feng; Tang, Jijun.

BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008. 2008. p. 34-38 4548631 (BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008; Vol. 1).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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N2 - Multiple sequence alignment is the most fundamental task in bioinformatics and computational biology. In this paper, we present a new algorithm to conduct multiple sequences alignment based on phylogenetic trees. It is widely accepted that a good phylogenetic tree can help produce high quality alignment, but the direct dynamic programming solution grows exponentially [13]. To overcome this problem, we first devise a procedure that can produce optimal alignment for three sequences and infer their common ancestor. We then extend the above procedure to compute the alignment of a given tree with more sequences by iteratively relabeling the internal nodes. We have implemented our algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM or BLOSUM series. We test our new method with biological and simulated datasets, and compare its performance with those of other popular multiple sequence alignment tools, including the widely used programs such as Clustalw and T-Coffee.

AB - Multiple sequence alignment is the most fundamental task in bioinformatics and computational biology. In this paper, we present a new algorithm to conduct multiple sequences alignment based on phylogenetic trees. It is widely accepted that a good phylogenetic tree can help produce high quality alignment, but the direct dynamic programming solution grows exponentially [13]. To overcome this problem, we first devise a procedure that can produce optimal alignment for three sequences and infer their common ancestor. We then extend the above procedure to compute the alignment of a given tree with more sequences by iteratively relabeling the internal nodes. We have implemented our algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM or BLOSUM series. We test our new method with biological and simulated datasets, and compare its performance with those of other popular multiple sequence alignment tools, including the widely used programs such as Clustalw and T-Coffee.

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Yue F, Tang J. A new approach for tree alignment based on local re-optimization. In BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008. 2008. p. 34-38. 4548631. (BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008). https://doi.org/10.1109/BMEI.2008.290