Annotation inconsistencies beyond sequence similarity-based function prediction – phylogeny and genome structure

Annotation inconsistencies beyond sequence similarity-based function prediction – phylogeny and genome structure

The function annotation process in computational biology has increasingly shifted from the traditional characterization of individual biochemical roles of protein molecules to the system-wide detection of entire metabolic pathways and genomic structures. The so-called genome-aware methods broaden misannotation inconsistencies in genome sequences beyond protein function assignments, encompassing...

Sequence- and Structure-Based Functional Annotation

The Prediction of Membrane Protein Structure and Genome Structural Annotation

New methods, essentially based on hidden Markov models (HMM) and neural networks (NN), can predict the topography of both beta-barrel and all-alpha membrane proteins with high accuracy and a low rate of false positives and false negatives. These methods have been integrated in a suite of programs to filter proteomes of Gram-negative bacteria, searching for new membrane proteins.

Genome Annotation and Protein Structure

Structural genomics aims to provide a goodexperimental structure or computational model of everytractable protein in a complete genome. Underlying thisgoal is the immense value of protein structure,especially in permitting recognition of distantevolutionary relationships for proteins whose sequenceanalysis has failed to find any significant homologue. Aconsiderable f...

Beyond the Sequence: Cellular Organization of Genome Function

Genomes are more than linear sequences. In vivo they exist as elaborate physical structures, and their functional properties are strongly determined by their cellular organization. I discuss here the functional relevance of spatial and temporal genome organization at three hierarchical levels: the organization of nuclear processes, the higher-order organization of the chromatin fiber, and the s...