CEMAsuite, is an interactive Java-based application with the ability to (i) construct a codon-equivalent multiple alignment (CEMA) from a protein multiple sequence alignment (MSA) file, (ii) generate and score each position in the consensus DNA sequence using multiple algorithms, (iii) design single-degeneracy primer backbones using Primer3 (Untergasser et al. 2012), (iv) estimate the stability of degenerate primers on each of the coding sequences within the CEMA, and (v) export intermediate results in various formats. The goal of CEMAsuite is to aid in the design of minimum-degeneracy primer sets which are robust enough for the assay at hand, while retaining as much specificity and product homology as possible.
admin: cemasuite@gmail.com
Features
- Generate codon-equivalent multiple alignments (CEMAs)
- Design consensus primers using score-weighted Primer3
- Analyze primer-template interactions at specific conditions
- Add degeneracy as needed
- Export intermediate results in various formats
Project Samples
License
GNU General Public License version 3.0 (GPLv3)Follow CEMAsuite
User Reviews
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Despite of the good software presentation and screenshots, I was unable to use it because I needed to design degenerate primers based on DNA sequences instead of protein sequences. Please add this option.