ProtParCon : A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid Replacements

Genes
Fei YuanDan Graur

Abstract

Studying parallel and convergent amino acid replacements in protein evolution is frequently used to assess adaptive evolution at the molecular level. Identifying parallel and convergent replacements involves multiple steps and computational routines, such as multiple sequence alignment, phylogenetic tree inference, ancestral state reconstruction, topology tests, and simulation of sequence evolution. Here, we present ProtParCon, a Python 3 package that provides a common interface for users to process molecular data and identify parallel and convergent amino acid replacements in orthologous protein sequences. By integrating several widely used programs for computational biology, ProtParCon implements general functions for handling multiple sequence alignment, ancestral-state reconstruction, maximum-likelihood phylogenetic tree inference, and sequence simulation. ProtParCon also contains a built-in pipeline that automates all these sequential steps, and enables quick identification of observed and expected parallel and convergent amino acid replacements under different evolutionary assumptions. The most up-to-date version of ProtParCon, including scripts containing user tutorials, the full API reference and documentation are publi...Continue Reading

References

Jun 1, 1992·Computer Applications in the Biosciences : CABIOS·D T JonesJ M Thornton
Jan 1, 1989·Folia primatologica; international journal of primatology·M D Pagel, P H Harvey
May 1, 1997·Molecular Biology and Evolution·J Zhang, S Kumar
Jun 1, 1997·Computer Applications in the Biosciences : CABIOS·A Rambaut, N C Grassly
Jun 25, 2002·Systematic Biology·Hidetoshi Shimodaira
Dec 9, 2003·Proceedings of the National Academy of Sciences of the United States of America·Austin L HughesMeredith Yeager
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Mar 28, 2007·Molecular Biology and Evolution·Giddy Landan, Dan Graur
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
May 6, 2008·Molecular Biology and Evolution·Arjun B PrasadEric D Green
Apr 21, 2009·Methods in Molecular Biology·Stéphane GuindonOlivier Gascuel
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Jun 17, 2011·BMC Evolutionary Biology·David M IrwinCaro-Beth Stewart
Oct 13, 2011·Molecular Systems Biology·Fabian SieversDesmond G Higgins
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
Dec 3, 2016·Nucleic Acids Research·UNKNOWN The UniProt Consortium

❮ Previous
Next ❯

Software Mentioned

TEST
PyPI
CODEML
msa
ProtParCon
Windows PowerShell
IDENTIFY
MUSCLE
NEWICK
EVOLVER

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.