ProbCons: probabilistic consistency-based multiple sequence alignment. To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however, is a difficult computational problem because of not only the high computational cost but also the lack of proper objective functions for measuring alignment quality. In this paper, we introduce probabilistic consistency, a novel scoring function for multiple sequence comparisons. We present ProbCons, a practical tool for progressive protein multiple sequence alignment based on probabilistic consistency, and evaluate its performance on several standard alignment benchmark data sets. On the BAliBASE, SABmark, and PREFAB benchmark alignment databases, ProbCons achieves statistically significant improvement over other leading methods while maintaining practical speed. ProbCons is publicly available as a Web resource.

References in zbMATH (referenced in 14 articles )

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  1. Arribas-Gil, Ana; Matias, Catherine: A time warping approach to multiple sequence alignment (2017)
  2. DeBlasio, Dan; Kececioglu, John: Parameter advising for multiple sequence alignment (2017)
  3. Nguyen, Ken; Guo, Xuan; Pan, Yi: Multiple biological sequence alignment. Scoring functions, algorithms and evaluation (2016)
  4. Mora-Gutiérrez, Roman Anselmo; Lárraga-Ramírez, María E.; Rincón-García, Eric A.; Ponsich, Antonin; Ramírez-Rodríguez, Javier: Adaptation of the method of musical composition for solving the multiple sequence alignment problem (2015)
  5. Daugelaite, Jurate; O’Driscoll, Aisling; Sleator, Roy D.: An overview of multiple sequence alignments and cloud computing in bioinformatics (2013)
  6. Saeed, Fahad; Perez-Rathke, Alan; Gwarnicki, Jaroslaw; Berger-Wolf, Tanya; Khokhar, Ashfaq: A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes (2012) ioport
  7. Fan, Xiaodan; Yuan, Yuan; Liu, Jun S.: The EM algorithm and the rise of computational biology (2010)
  8. Hara, Toshihide; Sato, Keiko; Ohya, Masanori: MTRAP: pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues (2010) ioport
  9. Edgar, Robert C.: Optimizing substitution matrix choice and gap parameters for sequence alignment (2009) ioport
  10. Schreiber, Fabian; Pick, Kerstin; Erpenbeck, Dirk; Wörheide, Gert; Morgenstern, Burkhard: Orthoselect: a protocol for selecting orthologous groups in phylogenomics (2009) ioport
  11. Sato, Kengo; Morita, Kensuke; Sakakibara, Yasubumi: PSSMTS: Position specific scoring matrices on tree structures (2008)
  12. Bernardes, Juliana S.; Davila, Alberto Mr; Costa, Vitor S.; Zaverucha, Gerson: Improving model construction of profile hmms for remote homology detection through structural alignment (2007) ioport
  13. Kruspe, Matthias; Stadler, Peter F.: Progressive multiple sequence alignments from triplets (2007) ioport
  14. Livesay, Dennis R.; Kidd, Patrick D.; Eskandari, Sepehr; Roshan, Usman: Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na^+ symporter family (2007) ioport