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.
Original language | English (US) |
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Pages (from-to) | 220-225 |
Number of pages | 6 |
Journal | Journal of Biomedical Informatics |
Volume | 58 |
DOIs | |
State | Published - Dec 1 2015 |
Bibliographical note
Publisher Copyright:© 2015 Elsevier Inc.
Keywords
- APOBEC3
- Alignment
- Hypermutation
- Indels (insertions/deletions)
- Viral sequences