Perform a Pairwise Sequence Alignment

MegAlign Pro supports local, global, semi-global, and chromosome-based pairwise alignment methods, as well as a specialized proprietary method for aligning cDNAs or other short sequences to a chromosome. Click here for descriptions and a comparison of the different methods.

How to perform a pairwise alignment:

Typical pairwise alignments involving sequences of similar lengths can only be performed when two sequences, and only two sequences, have been selected. A common workflow is to first perform a multiple alignment on an entire group of sequences. From the resulting Tree view, two closely related sequences can then be further analyzed by selecting them and performing a pairwise alignment. To learn how to perform this general type of pairwise alignment, see Pairwise alignment for sequences with similar lengths.

As of the Lasergene 17.5 release (July 2023), a new pairwise alignment procedure is available and mandatory for aligning short sequences like cDNAs to a chromosome or other extremely long sequence. For instructions, see Pairwise alignment of a short sequence to a chromosome

Pairwise alignment tutorials:

The following tutorials pertain to “typical” pairwise alignments (see the section above) and use data that can be downloaded from the DNASTAR website:

• Try It! – Follow a multiple alignment with Global pairwise alignments
• Try It! – Align transcripts to genes using Local and Global pairwise alignments
• Try It! – Use a Local pairwise alignment to find a gene within a genome