MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments

MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments

The increasing availability of structurally aligned protein families has made it possible to use statistical methods to discover regions of interpositional dependencies of residue identity. Such dependencies amongst residues often have structural or functional implications, and their discovery can supply valuable constraints that assist in the refinement of measured, or predicted molecular stru...

Detecting species-site dependencies in large multiple sequence alignments

Multiple sequence alignments (MSAs) are one of the most important sources of information in sequence analysis. Many methods have been proposed to detect, extract and visualize their most significant properties. To the same extent that site-specific methods like sequence logos successfully visualize site conservations and sequence-based methods like clustering approaches detect relationships bet...

Introducing statistical dependencies and structural constraints in variable-length sequence models

BPPS: An Algorithm for Analyzing Protein Sequence Alignments

selection (BPPS), which is based on a two-way mixture model and can simultaneously classify protein sequences into distinct subfamilies and select conserved positions that are characteristic of these subfamilies. When applied to P-loop GTPases, this revealed within Rab, Rho, Ras, and Ran a canonical network of molecular interactions centered on bound nucleotide. This network presumably performs...

Analyzing Concerns Using Class Member Dependencies

Basic programming language elements, such as classes and methods, cannot always faithfully modularize all the concerns programmers might wish to express in a program [6]. Often, some concerns end up scattered amongst the various classes, and tangled within a particular class. Various mechanisms have been proposed to help developers modularize concerns that cannot readily be encapsulated within ...