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

Hamid Alinejad-Rokny, Diako Ebrahimi

Research output: Contribution to journalArticle

1 Scopus citations

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 languageEnglish (US)
Pages (from-to)220-225
Number of pages6
JournalJournal of Biomedical Informatics
Volume58
DOIs
StatePublished - Dec 1 2015

Keywords

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

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