A method to avoid errors associated with the analysis of hypermutated viral sequences by alignment-based methods.

Alinejad-Rokny, Hamid, and Diako Ebrahimi. 2015. “A Method to Avoid Errors Associated With the Analysis of Hypermutated Viral Sequences by Alignment-Based Methods.”. Journal of Biomedical Informatics 58: 220-25.
Abstract

The human genome encodes for a family of editing enzymes known as APOBEC3 (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like3). They induce context dependent G-to-A changes, referred to as "hypermutation", in the genome of viruses such as HIV, SIV, HBV and endogenous retroviruses. Hypermutation is characterized by aligning affected sequences to a reference sequence. We show that indels (insertions/deletions) in the sequences lead to an incorrect assignment of APOBEC3 targeted and non-target sites. This can result in an incorrect identification of hypermutated sequences and erroneous biological inferences made based on hypermutation analysis.

Last updated on 01/11/2023
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