Multiple Protein Sequence Alignment Display with MSAReveal
From Proteopedia
MSAReveal.Org is a free, open-source tool for displaying multiple protein sequence alignments. It can be used to compare the sequence of a crystal structure with the genomic sequence. While viewing a structure in FirstGlance in Jmol, click Sequences (Molecule Information Tab). There, you can get the experimental sequence and the genomic sequence in one click each, ready for alignment and display.
An overview and introduction with snapshots is available in the MSAReveal Help.