This topic describes two methods that allow you to align only the portions of sequences the correspond to a particular gene or other feature. Other portions of the sequences are discarded or removed prior to alignment, making the alignment for that gene both faster and more accurate.

If you only need to trim a few sequences, you can do this manually. See Trim an individual sequence for instructions.

If you need to trim a larger number of sequences, we recommend doing this in SeqNinja, a batch file editor that is included in the same Lasergene package as MegAlign Pro. You can use SeqNinja’s Extract Features as Sequences template to batch extract the gene features (e.g., CDS, etc.) and save these as a separate set of sequences. You then add the trimmed sequences to MegAlign Pro and align them. If you are new to SeqNinja, Parts A and B of this tutorial show how to batch extract genes from multiple sequence files.

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