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arXiv · 2210.09842

MVP: Detection of motif-making and -breaking mutations

Afif Elghraoui·Faramarz Valafar
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Abstract

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.

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Afif Elghraoui, Faramarz Valafar. 2022-10-15. MVP: Detection of motif-making and -breaking mutations. https://arxiv.org/abs/2210.09842

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