There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accurate computational predictions are essential to annotate genomes in the first instance, and to provi...
Interdisciplinary sciences, computational life sciences
Aug 23, 2015
Representing the way forward, from functional genomics and its ontology to functional understanding and physiological model, in a computationally tractable fashion is one of the ongoing challenges faced by computational biology. To tackle the standpo...
Mammalian genome : official journal of the International Mammalian Genome Society
Jul 4, 2015
The Gene Ontology (GO) is an important component of modern biological knowledge representation with great utility for computational analysis of genomic and genetic data. The Gene Ontology Consortium (GOC) consists of a large team of contributors incl...
MOTIVATION: Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results.
The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets. Here, we provide an overview of machine learning ap...
BACKGROUND: Profiling gene expression in brain structures at various spatial and temporal scales is essential to understanding how genes regulate the development of brain structures. The Allen Developing Mouse Brain Atlas provides high-resolution 3-D...
The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation o...
BACKGROUND: Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones pro...
Functional annotation of the gigantic metagenomic data is one of the major time-consuming and computationally demanding tasks, which is currently a bottleneck for the efficient analysis. The commonly used homology-based methods to functionally annota...
As the number of sequenced bacterial genomes increases, the need for rapid and reliable tools for the annotation of functional elements (e.g., transcriptional regulatory elements) becomes more desirable. Promoters are the key regulatory elements, whi...