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

作者：Alinejad Rokny Hamid; Ebrahimi Diako^*

来源：Journal of Biomedical Informatics, 2015, 58: 220-225.

DOI：10.1016/j.jbi.2015.10.008

• Viral sequences
• Indels (insertions/deletions)
• Hypermutation
• APOBEC3
• Alignment

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.

• 出版日期2015-12