MASS: multiple structural alignment by secondary structures
نویسندگان
چکیده
منابع مشابه
MASS: 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 کاملMultiple 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 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...
متن کاملTurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs
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 ...
متن کاملImproving phonetic alignment by handling secondary sequence structures
In traditional alignment analyses, sequences are only compared with regard to their primary structure. Here, the term primary structure refers to the order order of segments, whereby segments are understood as the smallest units of a sequence which directly correspond to the characters of the alphabet from which the sequence is drawn. Apart from the primary structure, sequences can, however, al...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2003
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btg1012