Using hidden Markov models and observed evolution to annotate viral genomes

Bioinformatics
Stephen McCauley, Jotun Hein

Abstract

ssRNA (single stranded) viral genomes are generally constrained in length and utilize overlapping reading frames to maximally exploit the coding potential within the genome length restrictions. This overlapping coding phenomenon leads to complex evolutionary constraints operating on the genome. In regions which code for more than one protein, silent mutations in one reading frame generally have a protein coding effect in another. To maximize coding flexibility in all reading frames, overlapping regions are often compositionally biased towards amino acids which are 6-fold degenerate with respect to the 64 codon alphabet. Previous methodologies have used this fact in an ad hoc manner to look for overlapping genes by motif matching. In this paper differentiated nucleotide compositional patterns in overlapping regions are incorporated into a probabilistic hidden Markov model (HMM) framework which is used to annotate ssRNA viral genomes. This work focuses on single sequence annotation and applies an HMM framework to ssRNA viral annotation. A description of how the HMM is parameterized, whilst annotating within a missing data framework is given. A Phylogenetic HMM (Phylo-HMM) extension, as applied to 14 aligned HIV2 sequences is also...Continue Reading

References

Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Feb 1, 1995·Journal of Molecular Evolution·J Hein, J Støvlbaek
Apr 16, 1996·Proceedings of the National Academy of Sciences of the United States of America·A SanchezS T Nichol
Dec 1, 1996·Molecular Biology and Evolution·R T LarteyU Melcher
Jun 1, 1997·Journal of Molecular Evolution·A PavesiA Porati
Mar 12, 1999·The Journal of General Virology·V E VolchkovH Feldmann
Sep 11, 1999·Nucleic Acids Research·J Besemer, M Borodovsky
Aug 11, 2000·Evolution; International Journal of Organic Evolution·D C Krakauer
Feb 24, 2001·Doklady Biological Sciences : Proceedings of the Academy of Sciences of the USSR, Biological Sciences Sections·N N Kozlov
Jun 6, 2002·Trends in Genetics : TIG·Igor B RogozinEugene V Koonin
Jul 2, 2004·Molecular Biology and Evolution·Jakob Skou PedersenJotun Hein
Aug 3, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Adam Siepel, David Haussler
Sep 7, 2004·Bioinformatics·Andrew E Firth, Chris M Brown
Sep 28, 2004·Nucleic Acids Research·Jakob Skou PedersenJotun Hein

❮ Previous
Next ❯

Citations

Sep 13, 2007·Heredity·M Anisimova, D A Liberles
Jun 7, 2007·Bioinformatics·Wendy S W Wong, Rasmus Nielsen
Nov 10, 2009·Trends in Microbiology·Thomas SchoenfeldDavid Mead
Nov 13, 2012·PLoS Neglected Tropical Diseases·Jessica N RicaldiMichael A Matthias
Apr 10, 2012·PloS One·Atila IamarinoPaolo Marinho de Andrade Zanotto
Oct 9, 2007·Bioinformatics·Stephen McCauleyJotun Hein
Feb 1, 2007·Journal of Computer-aided Molecular Design·Marcus GastreichHolger Claussen
Oct 7, 2021·Nature Reviews. Genetics·Bradley W WrightPaul R Jaschke

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.