DuctApe statistics

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Citations per year

Number of citations per year for the bioinformatics software tool DuctApe
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Tool usage distribution map

This map represents all the scientific publications referring to DuctApe per scientific context
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Protocols

DuctApe specifications

Information


Unique identifier OMICS_25743
Name DuctApe
Software type Toolkit/Suite
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.17.12
Stability Stable
Requirements
biopython, numpy, scipy, matplotlib, scikits.learn, networkx, pyyaml, blast+
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Marco Galardini

Additional information


http://combogenomics.github.io/DuctApe/howto.html

Publication for DuctApe

DuctApe citations

 (12)
library_books

Integrated phenotypic genotypic approach to understand the influence of ultrasound on metabolic response of Lactobacillus sakei

2018
PLoS One
PMCID: 5784923
PMID: 29370210
DOI: 10.1371/journal.pone.0191053

[…] plate consists of an OD reading for each well, recorded at 15 min intervals over the 48 h incubation period. The data output for the control and ultrasound treated L. sakei cells were analysed using DuctApe software []. Negative controls (wells containing the inoculated Omnilog™ growth medium, but without any substrate for each PM plate was used to normalise differences in inoculums and redox dye […]

library_books

Ecology of cold environments: new insights of bacterial metabolic adaptation through an integrated genomic phenomic approach

2017
Sci Rep
PMCID: 5429795
PMID: 28404986
DOI: 10.1038/s41598-017-00876-4

[…] Lastly, we identified the number of phenotypic conditions provided by PM plates which resulted ‘linked’ to the genomic variability between PhTAC125 and PspTB41 by means of the DuctApe tool. We performed this analysis with AV values obtained from the PM experiments conducted at both 4 °C and 15 °C in order to highlight which metabolic differences were related to temperature […]

library_books

Two stable variants of Burkholderia pseudomallei strain MSHR5848 express broadly divergent in vitro phenotypes associated with their virulence differences

2017
PLoS One
PMCID: 5302386
PMID: 28187198
DOI: 10.1371/journal.pone.0171363

[…] r different statistical methods were used to analyze the data: the Biolog Phenotype MicroarrayTM analysis software; the opm and Pipeline packages based on R language, as described previously [–]; the DuctApe suite []; and a two-way ANOVA model using data normalized to positive control scores, as implemented in SAS® system's PROC GENMOD procedure. The results of these analyses were in general agree […]

library_books

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights

2017
BMC Genomics
PMCID: 5240218
PMID: 28095778
DOI: 10.1186/s12864-016-3382-y

[…] To compute the pangenome of Pseudoalteromonas genus, the dataset comprising the Pseudoalteromonas representatives was analyzed using the dgenome module of the Ductape suite [], which allowed a fast computation of the pangenome by using a pairwise BBH approach. The estimation of generalized pangenome metrics, such as core genome and pangenome size was perfor […]

library_books

Phenotypic Profiling Reveals that Candida albicans Opaque Cells Represent a Metabolically Specialized Cell State Compared to Default White Cells

2016
MBio
PMCID: 5120136
PMID: 27879329
DOI: 10.1128/mBio.01269-16

[…] The resulting dye reduction values were imported into a PM analysis software suite (DuctApe [http://combogenomics.github.io/DuctApe/]) which calculates metabolic activities (). Five PM growth curve parameters from each data set were extracted from the raw data—length of the lag phase […]

library_books

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

2016
Nat Commun
PMCID: 4961836
PMID: 27447951
DOI: 10.1038/ncomms12219

[…] oti RmP2754 (ΔB180) and a second wild-type control were inoculated from liquid M9-glucose cultures as RmP2754 grew poorly when inoculated directly from an agar plate. Data analysis was performed with DuctApe. Activity index (AV) values were calculated following subtraction of the blank well from the experimental wells, whereas plots of the growth curves are of the unblanked data. Growth with each […]


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DuctApe institution(s)
Department of Biology, University of Florence, Florence, Italy; Interdisciplinary Research Institute USR3078, CNRS-Université Lille Nord de France, Villeneuve d'Ascq, France; Consiglio per la Ricerca e la sperimentazione in Agricoltura, Centro di Ricerca per lo studio delle Relazioni tra Pianta e Suolo (CRA-RPS), Rome, Italy; Consiglio per la Ricerca e la sperimentazione in Agricoltura, Centro di Ricerca per l’Agrobiologia e la Pedologia (CRA-ABP), Florence, Italy
DuctApe funding source(s)
Supported by the Italian Ministry of Research (PRIN 2008 research grant contract No. TCKNJL, “Il pangenoma di Sinorhizobium meliloti: L’uso della genomica per il miglioramento agronomico dell’erba medica”) and by the project MARKERINBIO (DM 8348, 5/27/2010).

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