PFASUM: a substitution matrix from Pfam structural alignments
نویسندگان
چکیده
منابع مشابه
Glycan Linkage Substitution Matrix Rooted on Tree Alignments
Glycans are chains of monosaccharides, known to be extremely vital for the development and functioning of multi-cellular organisms. Matching and alignment algorithms for glycans were introduced based on proven efficient methods in bioinformatics for protein sequences [2]. These algorithms consequently can be taken advantage of in the form of statistical analyses. These algorithms were designed ...
متن کاملPfam: multiple sequence alignments and HMM-profiles of protein domains
Pfam contains multiple alignments and hidden Markov model based profiles (HMM-profiles) of complete protein domains. The definition of domain boundaries, family members and alignment is done semi-automatically based on expert knowledge, sequence similarity, other protein family databases and the ability of HMM-profiles to correctly identify and align the members. Release 2.0 of Pfam contains 52...
متن کاملA Protein Structural Alphabet and Its Substitution Matrix CLESUM
By using a mixture model for the density distribution of the three pseudobond angles formed by Cα atoms of four consecutive residues, the local structural states are discretized as 17 conformational letters of a protein structural alphabet. This coarse-graining procedure converts a 3D structure to a 1D code sequence. A substitution matrix between these letters is constructed based on the struct...
متن کاملExtracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach
MOTIVATION Multiple structural alignments (MSTAs) provide position-specific information on the sequence variability allowed by protein folds. This information can be exploited to better understand the evolution of proteins and the physical chemistry of polypeptide folding. Most MSTA methods rely on a pre-computed library of pairwise alignments. This library will in general contain conflicting r...
متن کاملPfam: a comprehensive database of protein domain families based on seed alignments.
Databases of multiple sequence alignments are a valuable aid to protein sequence classification and analysis. One of the main challenges when constructing such a database is to simultaneously satisfy the conflicting demands of completeness on the one hand and quality of alignment and domain definitions on the other. The latter properties are best dealt with by manual approaches, whereas complet...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2017
ISSN: 1471-2105
DOI: 10.1186/s12859-017-1703-z