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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 <>

Publication for Annotation Retrieval of Gene Ontology Terms

Argot in pipelines

 (3)
2017
PMCID: 5286417
PMID: 28145490
DOI: 10.1038/srep41394

[…] and the publicly available assemblies without annotation were annotated by the prokaryotic genome annotation system (prokka) pipeline. functional annotation of the predicted proteins was obtained by argot2. protein domains of each gene were identified by pfam_scan.pl v1.5 by comparing against pfam v27.0. the replication origin (oric) regions of bacterial genomes were predicted by the online […]

2016
PMCID: 4882050
PMID: 27228164
DOI: 10.1371/journal.pone.0156018

[…] gene ontology terms using the panther db [,], and the overrepresentation test was performed using a p-value < 0.05. those proteins that could not be annotated using panther were annotated with argot2 (total score > 200) [–]. the sub-cellular location of some proteins was predicted using cello v2.5 [,], and antigenicity was predicted using the kolaskar and tongaonkar antigenicity scale […]

2015
PMCID: 4437048
PMID: 25989346
DOI: 10.1038/srep09683

[…] by setting the following parameters: e-value-hit-filter: 1.0 e−3; annotation cut-off: 55; go weight: 5; hsp-hit coverage cut-off: 0., the es proteins were also mapped to gene ontology terms using argot2 by setting the total score (ts) to ≥200. additionally, es proteins were associated to protein families and domains through interproscan. blast2go was used to identify the statistically […]


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Argot in publications

 (28)
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] 35,747 predicted proteins against the uniref90 database. after filtering (evalue <0.00001 and bitscore >50), this yielded valid uniref protein names for 14,681 transcripts. separately, we used argot2 to obtain gene ontology (go) terms for our transcriptome, yielding 6107 unique go terms for 15,991 transcripts, with a mean of 5.2 go terms per annotated transcript. after removing go terms […]

PMCID: 5662880
PMID: 29123525
DOI: 10.3389/fimmu.2017.01382

[…] 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., unless specified, […]

PMCID: 5634658
PMID: 28945737
DOI: 10.1371/journal.pntd.0005962

[…] genscript (usa)., 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 […]

PMCID: 5552327
PMID: 28797052
DOI: 10.1371/journal.pone.0182097

[…] values represent the total number or average (standard deviation)., for all genes, biological process (bp) terms and molecular function (mf) terms were predicted using bmrf [–] for bp terms and argot2 [] for mf terms. the average number of bp terms per trait ranges from 958 to 1,106, and that of mf terms from 162 to 259; the average number per qtl region ranges from 494 to 632 for bp […]

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

[…] 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 […]


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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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