Accuracy analysis of multiple structure alignments
نویسندگان
چکیده
منابع مشابه
Accuracy of multiple sequence alignments as assessed by reference to structural alignments
In the last 20 years, many multiple-sequence alignment programs based on various principles have been developed. Continuous e orts have been devoted to solve two major problems: (1) how to evaluate the 'goodness' of an alignment, and (2) how to get the alignment with the optimal score. These problems are tightly interrelated, and other criteria are needed to objectively assess reliability of a ...
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l/sing a new database of 20 proteins not included in any of the previously used training datasets, we have incorporated multiple alignment information from homologous proteins into two well-characterized prediction methods: COMBINE (a jury method) and the Q-L (or quadratic-logistic) method. It is found that the increase in accuracy from the use of related proteins is similar for both methods (5...
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Secondary structure prediction methods are widely used bioinformatics algorithms providing initial insights about protein structure from sequence information. Significant efforts to improve the prediction accuracy over the past years were made, specially the incorporation of information from multiple sequence alignments. This motivated the search for the factors contributing for this improvemen...
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The relative performances of four strategies for aligning a large number of protein sequences were assessed by referring to corresponding structural alignments of 54 independent families. Multiple sequence alignment of a family was constructed by a given method from the sequences of known structures and their homologues, and the subset consisting of the sequences of known structures was extract...
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Although multiple sequence alignments (MSAs) are essential for a wide range of applications from structure modeling to prediction of functional sites, construction of accurate MSAs for distantly related proteins remains a largely unsolved problem. The rapidly increasing database of spatial structures is a valuable source to improve alignment quality. We explore the use of 3D structural informat...
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ژورنال
عنوان ژورنال: Protein Science
سال: 2009
ISSN: 0961-8368
DOI: 10.1002/pro.213