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Protocols

Argot specifications

Information


Unique identifier OMICS_19922
Name Argot
Alternative names Annotation Retrieval of Gene Ontology Terms, Argot2
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Some sequences.
Input format FASTA
Computer skills Basic
Version 2.5
Stability Stable
Maintained Yes

Maintainer


  • person_outline Stefano Toppo

Publications for Annotation Retrieval of Gene Ontology Terms

Argot citations

 (34)
library_books

Strong phenotypic plasticity limits potential for evolutionary responses to climate change

2018
Nat Commun
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] ) analyses in Babelomics v. 5, using the FatiScan module. As input, we used lists of genes (and their fold change) that were significantly season-biased in thorax, abdomen or both body parts, and the Argot2 GO annotation file. The GSE analyses yield a log odds ratio for enrichment associated with each GO term, with the same sign as fold change values in expression: positive for GO terms enriched a […]

library_books

Transcriptome and Cell Physiological Analyses in Different Rice Cultivars Provide New Insights Into Adaptive and Salinity Stress Responses

2018
Front Plant Sci
PMCID: 5844958
PMID: 29556243
DOI: 10.3389/fpls.2018.00204

[…] To expand the functional annotation of rice genes, the entire set of transcripts was annotated with the Argot web server (, ; ), which assigned Gene Ontology terms to each input sequence (Gene Ontology Annotation database downloaded on 2013-12-29, PFAM release 27.0). This procedure provided novel annota […]

library_books

Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design

2017
Front Immunol
PMCID: 5662880
PMID: 29123525
DOI: 10.3389/fimmu.2017.01382

[…] the corresponding COG cluster. For background proteomes and non-protective proteins, the COG cluster identifiers were retrieved directly from the UniProt database.The PAg sequences were submitted to Argot2 web server for GO annotation prediction (). The GO information of non-protective proteins and background proteomes were directly downloaded from UniProt database. […]

call_split

Quantitative multiplexed proteomics of Taenia solium cysts obtained from the skeletal muscle and central nervous system of pigs

2017
PLoS Negl Trop Dis
PMCID: 5634658
PMID: 28945737
DOI: 10.1371/journal.pntd.0005962
call_split See protocol

[…] Proteins from the host (Sus scrofa) were annotated using the PantherGo algorithm [, ]; in the case of T. solium proteins, only proteins with a P-value<0.01 were submitted to Argot2 algorithm [–] using a threshold of 200. Disulfide bonds, N-linked glycosylation sites, transmembrane regions, signal peptides, and GPI-anchoring sites were predicted for selected proteins using […]

call_split

Similarities between plant traits based on their connection to underlying gene functions

2017
PLoS One
PMCID: 5552327
PMID: 28797052
DOI: 10.1371/journal.pone.0182097
call_split See protocol

[…] To predict the biological process (BP) terms for each gene, BMRF was applied as described [–]. Predictions of molecular function (MF) terms were obtained with argot2 [], using default settings. For the sets of genes contained in QTL regions associated with a particular trait, the occurrence of BP or MF terms was compared with the overall occurrence of these […]

library_books

Mapping and characterization of G quadruplexes in Mycobacterium tuberculosis gene promoter regions

2017
Sci Rep
PMCID: 5515968
PMID: 28720801
DOI: 10.1038/s41598-017-05867-z

[…] e classified according to their functional category as reported in TubercuList. In addition, a de novo function prediction based on Gene Ontology (GO) annotations was performed with the online server Argot2.5 to expand already available annotations and potentially define functions for those genes that are still hypothetical/unknown (Supplementary File  ‘Function prediction’). Globally, 35 genes ou […]


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Argot institution(s)
Department of Molecular Medicine, University of Padova, Padova, Italy; Istituto Agrario San Michele all’Adige Research and Innovation Centre, Foundation Edmund Mach, Trento, Italy
Argot funding source(s)
Supported by ‘‘progetto d’Ateneo” PRAT CPDA138081/13, Grant ‘‘assegno senior” and ‘‘bando giovani studiosi” GRIC13AAI9 from University of Padova.

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