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DegePrime specifications

Information


Unique identifier OMICS_20459
Name DegePrime
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Mac OS
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Anders Andersson

Publication for DegePrime

DegePrime citations

 (3)
library_books

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

2017
Front Microbiol
PMCID: 5591341
PMID: 28928718
DOI: 10.3389/fmicb.2017.01561

[…] al., ; Stoeck et al., ; Hugerth et al., ), fungal ITS (Martin and Rygiewicz, ; Manter and Vivanco, ; Toju et al., ; Op De Beeck et al., ) and many other genes. PrimerProspector (Walters et al., ) and DegePrime (Hugerth et al., ) are examples of computer programs that can aid in the design of broad taxonomic primers. DegePrime finds the primers with maximal taxonomic coverage while controlling the […]

library_books

Design and evaluation of primers targeting genes encoding NO forming nitrite reductases: implications for ecological inference of denitrifying communities

2016
Sci Rep
PMCID: 5155301
PMID: 27966627
DOI: 10.1038/srep39208

[…] aligned the 454 and 110 full-length nirK and nirS sequences from complete genomes using the automatic structure guided alignment implemented in t-coffee expresso. For primer design we used HYDEN and DegePrime, which resulted in a total of 77 nirS and 79 nirK primer candidates (). To this dataset, we added the most commonly used primers for both genes () and the clade-specific primers recently dev […]

library_books

Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia

2014
PLoS One
PMCID: 3995771
PMID: 24755918
DOI: 10.1371/journal.pone.0095567

[…] n their annotation. After first trimming the alignment to only include positions represented by 90% of the sequences (while maintaining information on where nucleotides had been removed), the program DegePrime (https://github.com/EnvGen/DEGEPRIME; Hugerth et al. submitted) was used to generate 18 bases long degenerate primers at every alignment position, with maximum degeneracy 12. From these, the […]

Citations

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DegePrime institution(s)
KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden; Karolinska Institute, Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Stockholm, Sweden; Department of Preparedness, Swedish Institute for Communicable Disease Control, Stockholm, Sweden; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
DegePrime funding source(s)
Supported by the Swedish Research Councils VR (grant 2011-5689), FORMAS (grant 2009-1174), and EC BONUS project BLUEPRINT, partially funded by FORMAS through grants; and EcoChange grant.

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