2008
DOI: 10.1093/nar/gkn176
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High-throughput functional annotation and data mining with the Blast2GO suite

Abstract: Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annot… Show more

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Cited by 3,812 publications
(3,088 citation statements)
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References 39 publications
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“…Proteins were classified according to Gene Ontology (GO) categories using the software Blast2GO basic version 4.0.7 [27] and Pfam using HMMER v3.1b1 [28]. Putative signal peptides and transmembrane domain(s) were predicted using the programs CD-Search tool [29] and SignalP [30].…”
Section: Methodsmentioning
confidence: 99%
“…Proteins were classified according to Gene Ontology (GO) categories using the software Blast2GO basic version 4.0.7 [27] and Pfam using HMMER v3.1b1 [28]. Putative signal peptides and transmembrane domain(s) were predicted using the programs CD-Search tool [29] and SignalP [30].…”
Section: Methodsmentioning
confidence: 99%
“…LOSITAN was run in pairs, considering three scenarios: Semideciduous Forest versus Rainforest, Semideciduous Forest versus Restinga Forest, and Rainforest versus Restinga Forest, using the parameter setting of 100,000 simulations, confident interval of 0.95, and false discovery rate (FDR) of 0.1. Outlier SNPs were used in nucleotide searches with BLASTx against the genomic database of the National Center for Biotechnology Information, using blast2go (Gotz et al., 2008). For the sequences with significant BLAST hits, functional annotation was taken using the ontology system “gene ontology.”…”
Section: Methodsmentioning
confidence: 99%
“…When a direct link was not observed between UniProt accession and Gene Ontology (GO) accession, the equivalent human or mouse GO accession for that gene was taken with the assumption that functional classification would not vary too widely between species. Multilevel GO term analysis was performed by the Blast2GO program (Conesa et al, 2005;Götz et al, 2008) under default settings (minimum cutoff 1.0E-04 Blast X) and were filtered by annotation score.…”
Section: Data Acquisition and Statistical Analysismentioning
confidence: 99%