a.r.g.o.t.2

We present a novel method called Argot2 (Annotation Retrieval of Genel Ontology Terms), that is able to quickly process thousands of sequences for functional inference. The tool exploits a combined approach based on the clustering process of GO terms dependent on their semantic similarities and a weighting scheme which assesses retrieved hits sharing a certain degree of biological features with the sequence to annotate. These hits may be obtained by different methods as BLAST, HMMER and so on. In the present web server we allow users to interact with Argot2 in different ways according to specific needs and expertise.

If you use our service, please cite:

  • Fontana P, Cestaro A, Velasco R, Formentin E, Toppo S.
    Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology.
    PLoS One. 2009;4(2):e4619. Epub 2009 Feb 27. PubMed PMID: 19247487; PubMed Central PMCID: PMC2645684.

  • Falda M., Toppo S., Pescarolo A., Lavezzo E., Di Camillo B., Facchinetti A., Cilia E., Velasco R., Fontana P.
    Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.
    BMC bioinformatics, 13(4). 2012.

  • Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Skunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Smuc T, Kourmpetis YA, van Dijk AD, Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.
    A large-scale evaluation of computational protein function prediction.
    Nat Methods. 2013 Jan 27. doi: 10.1038/nmeth.2340. PubMed PMID: 23353650; PubMed Central PMCID: PMC3584181.

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