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|Interface||Command line interface|
|Restrictions to use||None|
|Operating system||Mac OS|
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- person_outline Anders Andersson
Publication for DegePrime
Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing
[…] 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 […]
Design and evaluation of primers targeting genes encoding NO forming nitrite reductases: implications for ecological inference of denitrifying communities
[…] 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 […]
Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia
[…] 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 […]
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