Rezan Topaloglu,Thierry Vilboux, Turgay Coskun, Fatih Ozaltin, Brad Tinloy, Meral Gunay-Aygun, Aysin Bakkaloglu, Nesrin Besbas, Lambert van den Heuvel, Robert Kleta, William A. Gahl. Ped Neph (2011): 6p.
"The most popular request I receive in the DNA core lab is: find the good clone among this group of 'candidate' minipreps. Alignment of ABI data files against a 'reference' sequence (template file) quickly eliminates defectives by showing not only base changes but the consequences to the protein translation.
The second most popular request is: validate this new maxiprep so it can be given to ... or used for ... or expressed in ... Rapid assembly and editing of total plasmid sequence and then comparison to the reference file on record is all done in Sequencher.
The third most popular request is: compare this library of (protein improvement) mutants and tell me which ones have protein changes. This is done by alignment in Sequencher and then formatting the Summary view to display the resulting changes in protein translation.
For my own projects, I use Sequencher as a very general multiple-alignment sequence editor. Most recently, I've been using it to make comparisons of genes retrieved from the databases for cross-species cDNA cloning. Showing regions of homology at the protein level and then having the colinear DNA sequence presented in the same view (Summary window) helps find regions suitable for primer design. Turning on the Matching Bases/Residues as Dashes quickly shows regions of homology and divergence. I design primers to either or both depending on the project.
Dean Regier, Research Scientist DNA core laboratories
"Sequencher 4.10.1 contains a new feature that keeps track of protein and cDNA numbering in DNA assemblies. This ability greatly simplifies the task of comparing your experimental data to a genomic DNA reference when looking for mutations or other changes. This feature alone reinforces Sequencher as one of the premier tools for sequence analysis.