  Background: DNA, RNA, and protein sequence motifs can be recognition sites
for biological functions such as regulation, DNA base modification, and
molecular binding in general. The gain and loss of such motifs can carry
important consequences. When comparing sequences, the analysis of individual
variants does not impart an understanding of the impact on these sites. Rather,
only when these variants considered together with their neighbors and the
original sequence context does this become possible.
  Results: The motif-variant probe (mvp) makes this consideration, counting
instances of user-specified sequence motifs before and after mutation and
reports those that result in motif gain or loss. mvp can perform a similar
analysis for proteins with amino acid variant data. The software is freely
available at https://lpcdrp.gitlab.io/mvp and also installable with the conda
package manager.
  Conclusions: The ability to easily search for variants affecting any motif,
together with the simultaneous consideration of neighboring variants makes mvp
a versatile tool to aid in a less-frequented dimension of comparative genomics.
