@article {21335611,
	title = {B2G-FAR, a species centered GO annotation repository.},
	journal = {Bioinformatics (Oxford, England)},
	volume = {27},
	number = {7},
	year = {2011},
	month = {2011 Feb 18},
	pages = {919-924},
	abstract = {<p>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 the 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://b2gfar.bioinfo.cipf.es. CONTACT: aconesa@cipf.es, sgoetz@cipf.es.</p>},
	author = {G{\"o}tz, Stefan and Arnold, Roland and Sebasti{\'a}n-Leon, Patricia and Mart{\'\i}n-Rodr{\'\i}guez, Samuel and Tischler, Patrick and Jehl, Marc-Andr{\'e} and Joaqu{\'\i}n Dopazo and Rattei, Thomas and Ana Conesa}
}
@article {19906725,
	title = {SIMAP{\textendash}a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.},
	journal = {Nucleic acids research},
	volume = {38},
	year = {2010},
	month = {2010 Jan},
	pages = {D223-6},
	abstract = {<p>The prediction of protein function as well as the reconstruction of evolutionary genesis employing sequence comparison at large is still the most powerful tool in sequence analysis. Due to the exponential growth of the number of known protein sequences and the subsequent quadratic growth of the similarity matrix, the computation of the Similarity Matrix of Proteins (SIMAP) becomes a computational intensive task. The SIMAP database provides a comprehensive and up-to-date pre-calculation of the protein sequence similarity matrix, sequence-based features and sequence clusters. As of September 2009, SIMAP covers 48 million proteins and more than 23 million non-redundant sequences. Novel features of SIMAP include the expansion of the sequence space by including databases such as ENSEMBL as well as the integration of metagenomes based on their consistent processing and annotation. Furthermore, protein function predictions by Blast2GO are pre-calculated for all sequences in SIMAP and the data access and query functions have been improved. SIMAP assists biologists to query the up-to-date sequence space systematically and facilitates large-scale downstream projects in computational biology. Access to SIMAP is freely provided through the web portal for individuals (http://mips.gsf.de/simap/) and for programmatic access through DAS (http://webclu.bio.wzw.tum.de/das/) and Web-Service (http://mips.gsf.de/webservices/services/SimapService2.0?wsdl).</p>},
	author = {Rattei, Thomas and Tischler, Patrick and G{\"o}tz, Stefan and Jehl, Marc-Andr{\'e} and Hoser, Jonathan and Arnold, Roland and Ana Conesa and Mewes, Hans-Werner}
}
