The Multiple Sequence Viewer is a great tool, but what I'm missing is reporting of % identity and % positives (as in Prime) when doing a multiple sequence alignment on imported sequences. Is there a way to see this information?

In the MSV Settings menu there are two options: "Display Percentage Identity" and "Display Percentage Similarity". These commands will display identity and similarity in a column on the right side, calculated with respect to a reference sequence. The reference sequence can be set by right-clicking on a sequence name and choosing "Set as Reference". (From Suite 2011, the reference sequence is now called the query sequence).

Reporting of pairwise sequence identity between all sequences is available starting with the Suite 2010 release.

Keywords: pairwise sequence identity, MSV settings, Display Percentage Identity, Display Percentage Similairty, Maestro

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