Calculating and scoring high quality multiple flexible protein structure alignments
نویسندگان
چکیده
منابع مشابه
Suboptimal Local Alignments Across Multiple Scoring Schemes
Sequence alignment algorithms have a long standing tradition in bioinformatics. In this paper, we formulate an extension to existing local alignment algorithms: local alignments across multiple scoring functions. For this purpose, we use the Waterman-Eggert algorithm for suboptimal local alignments as template and introduce two new features therein: 1) an alignment of two strings over a set of ...
متن کاملFinding Winner Alignments with Multiple Scoring Matrices
How to align two given sequences properly is a fundamental problem in bioinformatics. In the sequence alignment problem, the most essential thing that directly affects the resulting alignment is the scoring matrix. There are a variety of scoring matrices used for alignment, and each of them has its own purpose in biosequence alignment. It seems unlikely that an alignment is optimal for each sco...
متن کاملPROMALS3D: a tool for multiple protein sequence and structure alignments
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...
متن کاملUsing de novo protein structure predictions to measure the quality of very large multiple sequence alignments
MOTIVATION Multiple sequence alignments (MSAs) with large numbers of sequences are now commonplace. However, current multiple alignment benchmarks are ill-suited for testing these types of alignments, as test cases either contain a very small number of sequences or are based purely on simulation rather than empirical data. RESULTS We take advantage of recent developments in protein structure ...
متن کاملQUASAR - scoring and ranking of sequence-structure alignments
SUMMARY Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult pro...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2016
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btw300