Gene Ontology annotation software tools | High-throughput sequencing data analysis
Gene ontologies are unified vocabularies and representations for genes and gene products across all living organisms. Gene annotation is of great importance for identification of their function or host species, particularly after genome sequencing. Gene ontology software tools are used for management, information retrieval, organization, visualization and statistical analysis of large sets of genes.
A web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. This is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (e.g. by level of expression or of differential expression).
Analyzes interrelations of term and functional groups in biological networks. ClueGO offers the possibility to visualize terms corresponding to a list of genes and allows the comparison of functional annotations of two clusters. This Cytoscape plug-in contains Gene Ontology (GO) terms and KEGG/BioCarta pathways. This software can be also applied to new organisms, identifier types and annotation sources.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Predicts the function of genes and gene sets. GeneMANIA is used for probing of gene function and revealing pairwise connections linking genes in yeast, fly, worm, human and other species. It allows users to construct networks from gene lists for custom organisms and network data. The prediction performed provides a method for leveraging functionally informative associations to explore bacterial gene function.
Permits functional annotation, management, and data mining of novel sequence data. Blast2GO is based on the utilization of common controlled vocabulary schemas, the gene ontology (GO). It takes in consideration similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations. This tool is suitable for plant genomics research. It generates functional annotation and assesses the functional meaning of their experimental results.
Serves for visualizing, comparing and plotting gene ontology (GO) annotation results. WEGO allows researchers to work with the directed acyclic graph structure of GO to simplify histogram creation of GO annotation results. Moreover, this program can be used for understanding GO annotations and supports the comparison between several gene datasets.
Allows users to obtain biological features/meaning associated with large gene or protein lists. DAVID can determine gene-gene similarity, based on the assumption that genes sharing global functional annotation profiles are functionally related to each other. It groups related genes or terms into functional groups employing the similarity distances measure. This tool takes into account the redundant and network nature of biological annotation contents.