A method to avoid errors associated with the analysis of hypermutated viral sequences by alignment-based methods.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 26494601.
- Also identified by DOI 10.1016/j.jbi.2015.10.008.
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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.
Medical subject headings
- Mutation
- Sequence Alignment
- Viruses