B2G-FAR, a species-centered GO annotation repository

Abstract

Motivation: Functional genomics research has expanded enormously in the last decade thanks to the cost reduction in high-throughput technologies and the development of computational tools that generate, standardize and share information on gene and protein function such as the Gene Ontology (GO). Nevertheless, many biologists, especially working with non-model organisms, still suffer from non-existing or low-coverage functional annotation, or simply struggle retrieving, summarizing and querying these data.Results: The Blast2GO Functional Annotation Repository (B2G-FAR) is a bioinformatics resource envisaged to provide functional information for otherwise uncharacterized sequence data and offers data mining tools to analyze a larger repertoire of species than currently available. This new annotation resource has been created by applying the Blast2GO functional annotation engine in a strongly high-throughput manner to the entire space of public available sequences. The resulting repository contains GO term predictions for over 13.2 million non-redundant protein sequences based on BLAST search alignments from the SIMAP database. We generated GO annotation for approximately 150 000 different taxa making available 2000 species with the highest coverage through B2G-FAR. A second section within B2G-FAR holds functional annotations for 17 non-model organism Affymetrix GeneChips.Conclusions: B2G-FAR provides easy access to exhaustive functional annotation for 2000 species offering a good balance between quality and quantity, thereby supporting functional genomics research especially in the case of non-model organisms.Availability: The annotation resource is available at http://www.b2gfar.org.Contact: aconesa@cipf.es; sgoetz@cipf.esSupplementary information: Supplementary data are available at Bioinformatics online.

Genomic and transcriptomic analyses of the medicinal fungusAntrodia cinnamomeafor its metabolite biosynthesis and sexual development

“…Gene ontology was identified by AmiGO v1.8 (51, 52) (E-value ≤1 × 10 −5 ). We mapped ACg proteins to InterPro domains and KEGG pathways using Blast2GO v2.7.0 (53,54).…”

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

“…To obtain further insights into the regulatory mechanisms involving miRNA pathways and their relevance concerning tissue-specificity, all the specific targets for each tissue (72 for leaves and 219 for phellem) were annotated using Blast2GO Conesa et al 2005;Götz et al 2011;Götz et al 2008). …”

Genome–wide Analysis of Ethylene Responsive Factor in Maize: An in Silico Approach

“…Attributes used to accomplish data analysis include; number of different motifs: 20, minimum motif width: 15, maximum motif width: 54 amino acids, distribution of the motif occurrence: zero or one per sequences. The gene ontology of ERF protein sequence was performed using BLAST GO (Conesa and Götz, 2008;Gotz et al, 2011) with default parameters. GO analysis of ZmERF described the biological process, species distribution, molecular function and cellular localization (Gotz et al, 2011 Location of all these genes on chromosomes is determined as per data of Phytozome and NCBI for instance, chromosome number, chromosome length and start position of gene.…”

“…The gene ontology of ERF protein sequence was performed using BLAST GO (Conesa and Götz, 2008;Gotz et al, 2011) with default parameters. GO analysis of ZmERF described the biological process, species distribution, molecular function and cellular localization (Gotz et al, 2011 Location of all these genes on chromosomes is determined as per data of Phytozome and NCBI for instance, chromosome number, chromosome length and start position of gene. Graphical map is made by designing scale on the longest chromosome basis (chromosome number 5), and gene position on chromosome is considered as the gene annotation: like GRMZM1.14, GRMZM1.4 and GRMZM6.5 for AC206031, AC206951 and GRMZM2G085964, respectively.…”