When should I use a pairwise sequence alignment?

Use pairwise alignment when you are only interested in comparing two sequences. Additionally, there are situations where a multiple sequence alignment (MSA) might help identify pairs for sequences or sub-sequences that are worth a more detailed, pairwise comparison.

Which is better, multiple or pairwise alignment?

Both have different goals. If you want to see the evolutionary relatedness of a group of sequences by creating and viewing a phylogenetic tree, multiple sequence alignment is the best choice. Pairwise alignment is the ideal choice for comparing two sequences in detail.

What are the different pairwise alignment methods offered and how do I know which one to use?

MegAlign Pro features three pairwise sequence alignment tools:

• Local Pairwise Alignment is designed specifically to find the highest scoring aligned segments of two sequences, even if the full extent of the two is not included in the final alignment.
• Global Pairwise Alignment doesn’t try to find the best scoring segment, but instead requires that the full extent of both sequences be included in their results. There is no requirement or guarantee that the best scoring pair of aligned segments from a local alignment will be aligned in a global alignment.
• Semi-Global Pairwise Alignment is a relatively new approach that is particularly suitable when the two sequences differ greatly in length. When that happens, the longer sequence will have overhangs on either end of the alignment. Since overhangs are represented with gaps, a global aligner will attempt to increase the match score and minimize accumulated gap penalties by aligning parts of the shorter sequence to overhanging sequence region(s). This effect can produce a number of unrealistic, usually small aligned segments spaced by gaps near the ends of the alignment. Semi-global alignment is designed to address this problem by not penalizing gaps in overhangs (aka “end gaps”).

How do I export an image of my pairwise sequence alignment?

File > Export Image > (View Name). to export an image of your alignment for publication as an Adobe PDF (.pdf), Microsoft PowerPoint-optimized (.pptx), PNG image (.png) or JPG image (.jpg, .jpeg) file.

Can I perform a pairwise alignment within my multiple sequence alignment?

Yes, it is sometimes helpful to run a pairwise alignment to resolve a confusing placement of gaps within a multiple alignment. To do this, select the two sequences of interest, right-click on either name and select Align Pairwise.