State of the art: refinement of multiple sequence alignments
| Autor: | Stephen H. Bryant, Anna R. Panchenko, Teresa M. Przytycka, Christopher J. Lanczycki, Paul A. Thiessen, Saikat Chakrabarti |
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| Jazyk: | angličtina |
| Rok vydání: | 2006 |
| Předmět: |
Sequence analysis
Computer science Sequence alignment computer.software_genre lcsh:Computer applications to medicine. Medical informatics Biochemistry Sensitivity and Specificity Protein structure Structural Biology Sequence Analysis Protein Databases Protein Molecular Biology lcsh:QH301-705.5 Sequence (medicine) Applied Mathematics Correction Computational Biology State (functional analysis) Markov Chains Computer Science Applications Protein Structure Tertiary lcsh:Biology (General) lcsh:R858-859.7 Programming Languages Data mining DNA microarray Algorithm computer Sequence Alignment Algorithms Software Research Article |
| Zdroj: | BMC Bioinformatics, Vol 7, Iss 1, p 499 (2006) BMC Bioinformatics BMC Bioinformatics, Vol 11, Iss 1, p 3 (2010) |
| ISSN: | 1471-2105 |
| Popis: | Background Accurate multiple sequence alignments of proteins are very important in computational biology today. Despite the numerous efforts made in this field, all alignment strategies have certain shortcomings resulting in alignments that are not always correct. Refinement of existing alignment can prove to be an intelligent choice considering the increasing importance of high quality alignments in large scale high-throughput analysis. Results We provide an extensive comparison of the performance of the alignment refinement algorithms. The accuracy and efficiency of the refinement programs are compared using the 3D structure-based alignments in the BAliBASE benchmark database as well as manually curated high quality alignments from Conserved Domain Database (CDD). Conclusion Comparison of performance for refined alignments revealed that despite the absence of dramatic improvements, our refinement method, REFINER, which uses conserved regions as constraints performs better in improving the alignments generated by different alignment algorithms. In most cases REFINER produces a higher-scoring, modestly improved alignment that does not deteriorate the well-conserved regions of the original alignment. |
| Databáze: | OpenAIRE |
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