Improvement of alignment accuracy utilizing sequentially conserved motifs.
Improvement of alignment accuracy utilizing sequentially conserved motifs.
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DOI：
10.1186/1471-2105-5-167
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发表时间：
2004-10-28
影响因子：
3
通讯作者：
Sowdhamini R
中科院分区：
文献类型：
--
作者：
Chakrabarti S;Bhardwaj N;Anand PA;Sowdhamini R
多序列比对算法是当今分子生物学中非常重要的工具。蛋白质的精确比对是几个领域的核心，如同源性建模，对接研究，理解进化趋势和结构-功能关系的研究。近年来，对已有的进展程序的改进和新的迭代算法的实现使这一领域发生了重大变化。我们报告的对齐算法，结合渐进动态算法，局部子结构对齐和迭代细化，以实现改进的，用户交互式的工具。大规模的基准研究表明，这个FMALIGN服务器产生的路线，除了保存功能和结构的保护，具有准确性相媲美的其他流行的多重比对程序。FMALIGN服务器允许用户在比对中将保守区域固定在等同位置，从而在很大程度上减少全局失准的机会。FMALIGN可在
Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology modelling, docking studies, understanding evolutionary trends and study of structure-function relationships. In recent times, improvement of existing progressing programs and implementation of new iterative algorithms have made a significant change in this field. We report an alignment algorithm that combines progressive dynamic algorithm, local substructure alignment and iterative refinement to achieve an improved, user-interactive tool. Large-scale benchmarking studies show that this FMALIGN server produces alignments that, aside from preservation of functional and structural conservation, have accuracy comparable to other popular multiple alignment programs. The FMALIGN server allows the user to fix conserved regions in equivalent position in the alignment thereby reducing the chance of global misalignment to a great extent. FMALIGN is available at