research-article

SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures

Authors:

Hongyi Zhou,

Yaoqi ZhouAuthors Info & Claims

Bioinformatics, Volume 21, Issue 18

Pages 3615 - 3621

https://doi.org/10.1093/bioinformatics/bti582

Published: 15 September 2005 Publication History

Abstract

Motivation: Multiple sequence alignment is an essential part of bioinformatics tools for a genome-scale study of genes and their evolution relations. However, making an accurate alignment between remote homologs is challenging. Here, we develop a method, called SPEM, that aligns multiple sequences using pre-processed sequence profiles and predicted secondary structures for pairwise alignment, consistency-based scoring for refinement of the pairwise alignment and a progressive algorithm for final multiple alignment.

Results: The alignment accuracy of SPEM is compared with those of established methods such as ClustalW, T-Coffee, MUSCLE, ProbCons and PRALINE _PSI in easy (homologs) and hard (remote homologs) benchmarks. Results indicate that the average sum of pairwise alignment scores given by SPEM are 7--15% higher than those of the methods compared in aligning remote homologs (sequence identity <30%). Its accuracy for aligning homologs (sequence identity >30%) is statistically indistinguishable from those of the state-of-the-art techniques such as ProbCons or MUSCLE 6.0.

Availability: The SPEM server and its executables are available on http://theory.med.buffalo.edu

Contact: [email protected]

Cited By

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Layeb ASelmane MElhoucine M(2013)A new greedy randomised adaptive search procedure for multiple sequence alignmentInternational Journal of Bioinformatics Research and Applications10.1504/IJBRA.2013.0546959:4(323-335)Online publication date: 1-Jun-2013
https://dl.acm.org/doi/10.1504/IJBRA.2013.054695
Kim EKececioglu J(2008)Learning Scoring Schemes for Sequence Alignment from Partial ExamplesIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2008.575:4(546-556)Online publication date: 1-Oct-2008
https://dl.acm.org/doi/10.1109/TCBB.2008.57
Lu YSze S(2007)Multiple sequence alignment based on profile alignment of intermediate sequencesProceedings of the 11th annual international conference on Research in computational molecular biology10.5555/1758222.1758242(283-295)Online publication date: 21-Apr-2007
https://dl.acm.org/doi/10.5555/1758222.1758242
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Index Terms

SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures
1. Applied computing
  1. Life and medical sciences
2. Theory of computation
  1. Design and analysis of algorithms
    1. Approximation algorithms analysis
      1. Scheduling algorithms
    2. Online algorithms
      1. Online learning algorithms
        Scheduling algorithms
  2. Theory and algorithms for application domains
    1. Machine learning theory
      1. Reinforcement learning
        Sequential decision making

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Published In

Bioinformatics Volume 21, Issue 18

September 2005

114 pages

ISSN:1367-4803

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Publisher

Oxford University Press, Inc.

United States

Publication History

Published: 15 September 2005

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Layeb ASelmane MElhoucine M(2013)A new greedy randomised adaptive search procedure for multiple sequence alignmentInternational Journal of Bioinformatics Research and Applications10.1504/IJBRA.2013.0546959:4(323-335)Online publication date: 1-Jun-2013
https://dl.acm.org/doi/10.1504/IJBRA.2013.054695
Kim EKececioglu J(2008)Learning Scoring Schemes for Sequence Alignment from Partial ExamplesIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2008.575:4(546-556)Online publication date: 1-Oct-2008
https://dl.acm.org/doi/10.1109/TCBB.2008.57
Lu YSze S(2007)Multiple sequence alignment based on profile alignment of intermediate sequencesProceedings of the 11th annual international conference on Research in computational molecular biology10.5555/1758222.1758242(283-295)Online publication date: 21-Apr-2007
https://dl.acm.org/doi/10.5555/1758222.1758242
Bilu YAgarwal PKolodny R(2006)Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise ComparisonsIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2006.533:4(408-422)Online publication date: 1-Oct-2006
https://dl.acm.org/doi/10.1109/TCBB.2006.53
Cutello VLee DNicosia GPavone MPrizzi I(2006)Aligning multiple protein sequences by hybrid clonal selection algorithm with insert-remove-gaps and blockshuffling operatorsProceedings of the 5th international conference on Artificial Immune Systems10.1007/11823940_25(321-334)Online publication date: 4-Sep-2006
https://dl.acm.org/doi/10.1007/11823940_25
Do CGross SBatzoglou S(2006)CONTRAlignProceedings of the 10th annual international conference on Research in Computational Molecular Biology10.1007/11732990_15(160-174)Online publication date: 2-Apr-2006
https://dl.acm.org/doi/10.1007/11732990_15

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Using the SPEM 2.0 kind-based extension mechanism to define the SPEM4MDE metamodel

Identification of human-specific transcript variants induced by DNA insertions in the human genome

A probabilistic method for the detection and genotyping of small indels from population-scale sequence data

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