Multiple structural alignment by secondary structures: Algorithm and applications
نویسندگان
چکیده
منابع مشابه
Multiple structural alignment by secondary structures: algorithm and applications.
We present MASS (Multiple Alignment by Secondary Structures), a novel highly efficient method for structural alignment of multiple protein molecules and detection of common structural motifs. MASS is based on a two-level alignment, using both secondary structure and atomic representation. Utilizing secondary structure information aids in filtering out noisy solutions and achieves efficiency and...
متن کاملMASS: multiple structural alignment by secondary structures
We present a novel method for multiple alignment of protein structures and detection of structural motifs. To date, only a few methods are available for addressing this task. Most of them are based on a series of pairwise comparisons. In contrast, MASS (Multiple Alignment by Secondary Structures) considers all the given structures at the same time. Exploiting the secondary structure representat...
متن کاملMUSTANG: a multiple structural alignment algorithm.
Multiple structural alignment is a fundamental problem in structural genomics. In this article, we define a reliable and robust algorithm, MUSTANG (MUltiple STructural AligNment AlGorithm), for the alignment of multiple protein structures. Given a set of protein structures, the program constructs a multiple alignment using the spatial information of the C(alpha) atoms in the set. Broadly based ...
متن کاملGraphClust: alignment-free structural clustering of local RNA secondary structures
MOTIVATION Clustering according to sequence-structure similarity has now become a generally accepted scheme for ncRNA annotation. Its application to complete genomic sequences as well as whole transcriptomes is therefore desirable but hindered by extremely high computational costs. RESULTS We present a novel linear-time, alignment-free method for comparing and clustering RNAs according to seq...
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This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions between all pairs of input sequences are iteratively estimated in TurboFold II ...
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ژورنال
عنوان ژورنال: Protein Science
سال: 2009
ISSN: 0961-8368
DOI: 10.1110/ps.03200603