Champuru 2: Improved Scoring of Alignments and a User-Friendly Graphical Interface.

Area of Science:

• Bioinformatics
• Molecular Biology
• Genomics

Background:

• Mixed Sanger sequencing generates complex chromatograms from multiple DNA templates.
• Previous tools like Champuru 1.0 had limited accessibility due to server decommissioning.
• Accurate deconvolution of mixed chromatograms is crucial for genetic analysis.

Purpose of the Study:

• To redevelop and enhance the Champuru software for analyzing mixed Sanger chromatograms.
• To improve the efficiency and accuracy of identifying DNA sequences in mixed samples.
• To provide a freely accessible and user-friendly tool for researchers.

Main Methods:

• Implementation of Champuru 2 using Haxe, transpiled to JavaScript for GUI and C++ for command-line versions.
• Development of sophisticated algorithms for computing alignment scores between forward and reverse traces.
• Statistical comparison of alignment scores against theoretical expectations to calculate p-values.

Main Results:

• Champuru 2 offers an improved graphical user interface and more efficient sequence alignment algorithms.
• The tool accurately detects likely alignment positions and calculates p-values for offset pairs.
• Champuru 2 allows analysis of alternative offset pairs beyond the most likely one detected.

Conclusions:

• Champuru 2 provides a robust and accessible solution for deconvoluting mixed Sanger sequencing data.
• The enhanced algorithms and statistical analysis improve the reliability of sequence determination.
• The web-based platform and command-line version cater to diverse user needs in molecular biology research.