Edge wander

In class today, we talked about the first Assemblethon paper. A student asked about the term “edge wander”, which comes from a paper by Ian Holmes and Richard Durbin. Figure 6 from the paper illustrates the basic idea.

Edge wander is a problem in multiple sequence alignments, and often scientists manually adjust alignments based on some heuristics that are not entirely clear to me. At last year’s Texas Protein Folding and Function Meeting, Patsy Babbitt mentioned in passing that manually adjusting multiple sequence alignments has become impractical as the number of available sequences in conserved protein families is exploding.