Argo Genome Browser protocols

View Argo Genome Browser computational protocol

Argo Genome Browser statistics

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Argo Genome Browser specifications

Information


Unique identifier OMICS_00902
Name Argo Genome Browser
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
License GNU Lesser General Public License version 3.0
Computer skills Medium
Version 1.0.31
Stability No
Maintained No

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Documentation


Publication for Argo Genome Browser

Argo Genome Browser in pipeline

2017
PMCID: 5577849
PMID: 28854898
DOI: 10.1186/s12864-017-4060-4

[…] the program tree-puzzle []. for pairwise syntenic analysis of genome structures, the scaffolds of the paired genomes of c. cicadae, c. militaris and i. fumosorosea were oriented by megablast and argo genome browser for dot plotting analysis []. blast score ratio (bsr) analysis was conducted to compare the difference between the paired genomes []. the normalized pairs of bsr indices […]


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Argo Genome Browser in publications

 (11)
PMCID: 5577849
PMID: 28854898
DOI: 10.1186/s12864-017-4060-4

[…] the program tree-puzzle []. for pairwise syntenic analysis of genome structures, the scaffolds of the paired genomes of c. cicadae, c. militaris and i. fumosorosea were oriented by megablast and argo genome browser for dot plotting analysis []. blast score ratio (bsr) analysis was conducted to compare the difference between the paired genomes []. the normalized pairs of bsr indices […]

PMCID: 5470051
PMID: 28659962
DOI: 10.3389/fpls.2017.01030

[…] dna elements in the promoter sequences (1.5-kb upstream of the 5′-utr) of tafba genes were annotated with plantcare (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/), and displayed in argo genome browser v1.0.31 (http://www.broadinstitute.org/annotation/argo/). the exon-intron structure of the tafba genes was determined by aligning the cdna sequences to the corresponding genomic […]

PMCID: 4619572
PMID: 26500719
DOI: 10.1186/s40793-015-0082-1

[…] sequence was then confirmed and the start of the sequence manually set to dnaa using gap4 tool from staden package []., genes were identified using prodigal v2.50 tool [] with manual curation in argo genome browser []. the predicted genes were translated and functionally annotated with description lines, gene ontology (go) classes and enzyme commission (ec) numbers with pannzer program [] […]

PMCID: 3981765
PMID: 24718683
DOI: 10.1371/journal.pone.0094126

[…] subjected to prediction of cis-acting regulatory dna elements using plantpan with the transcription factors selected from rice, maize and arabidopsis. the regulatory dna elements were displayed in argo genome browser v1.0.26 (http://www.broadinstitute.org/annotation/argo/)., spatio-temporal expression regulation of maize mterfs was investigated using the microarray data (zm37) […]

PMCID: 3484023
PMID: 22876864
DOI: 10.1186/1471-2164-13-382

[…] was performed independently with a combination of three gene prediction program, including genemark (v2.3), augustus (v2.3.1), and exonhunter. the gene models were selected and manually curated by argo genome browser (v 1.0.31, http://www.broadinstitute.org/annotation/argo/). the gene models were aligned using blastp against the protein sequence of b. cinerea and s. sclerotiorum ( […]


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Argo Genome Browser funding source(s)
Supported by National Institute of Allergy and Infectious Diseases, National Institutes of Health.

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