The Exelixis Lab

Enabling Research in Evolutionary Biology

ChromatoGate 1.2

A code for analyzing/editing chromatogram data by Nikos Alachiotis: Windows code available for download here

A manual with step-by-step instructions is available for download here PDF

when using the code please cite this paper.

ChromatoGate (CG) accelerates the process of detecting potential errors in DNA sequences that have been introduced/generated by Sanger sequencing.

To detect errors, CG starts from a multiple sequence alignment instead of inspecting every sequence and chromatogram separately prior to alignment. CG does not align nor change anything in the sequences, that is, it does not automatically remove potential sequencing errors.

It implements a series of user-controlled steps that are required in the multiple sequence alignment generation and correction process. During the alignment generation procedure (relying on any external MSA tool), the tool gathers information about alignment gaps, trimmed sequence edges, forward/reversed/consensus sequences, and corrections that have already been applied to the sequences by the user. Using this collected information, CG detects and reports chromatogram peaks to the user for thoses bases in the sequence alignment that have been identified as "problematic" based on a user-defined threshold.