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This page allows the identification of mutations in AB1 and get the corresponding amino acid mutation for both homogeneous and heterogeneous sites.
Whereas anything called differently or as a degenerate base in the AB1 automatic calling is interpreted, secondary peaks are only considered if they are above a given background noise threshold.
The noise is calculated from the average variation in secondary peaks. This is generally fairly unless there is a strong contaminant or there is a frameshift in part of the pool, which would be visible as a sudden increase in noise in the noise plot.
The app does not do a sophisticated alignments as there is no need —there should be one or two mutations different.
If you get garbage out, you may have a contaminant, in which case your best bet is to blast it to find out where it came from.
Where to from here?
This page is part of a series of apps designed to help you with your mutagenesis.
If you just used MutantCaller to assess the diversity of sequences, once you know your cloning worked, you can estimate the mutational load, bias and redundancy with the app Mutanalyst.
If you are unhappy with the mutational load (if any), you can always take a step back and replan your experiment, using the planner app.
If you just used MutantCaller to look at your winners from a selection, and are confused by the fact you got what looks like a good mutation and a bad one and would like to know the probability of having in the library one of those mutations without the other, then go to the Chances page.