Related Experiment Video
Updated: Jan 28, 2026
10:41
Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
Published on: June 24, 2019
8.8K
ProtParCon: A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid
Fei Yuan1, Hoa Nguyen2, Dan Graur3
1Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA. fyuan4@uh.edu.
Genes
|March 1, 2019
Summary
ProtParCon is a new Python package that simplifies identifying parallel and convergent amino acid replacements in protein evolution. This tool automates complex computational steps, aiding molecular evolution research.
Area of Science:
- Molecular Biology
- Evolutionary Biology
- Bioinformatics
Background:
- Assessing adaptive evolution at the molecular level often involves studying parallel and convergent amino acid replacements.
- Identifying these replacements requires complex computational workflows, including sequence alignment, phylogenetic inference, and ancestral state reconstruction.
Purpose of the Study:
- To present ProtParCon, a Python 3 package designed to streamline the identification of parallel and convergent amino acid replacements in orthologous protein sequences.
- To provide a unified interface for processing molecular data and automating key computational biology steps.
Main Methods:
- Integration of established bioinformatics programs for multiple sequence alignment, phylogenetic tree inference, and ancestral-state reconstruction.
- Development of a Python package (ProtParCon) with a built-in pipeline for automated analysis.
- Implementation of functions for sequence simulation to assess evolutionary assumptions.
Main Results:
- ProtParCon offers a common interface for users to handle molecular data and identify parallel and convergent amino acid replacements.
- The package automates sequential computational steps, enabling rapid identification of evolutionary patterns.
- It facilitates the comparison of observed and expected amino acid replacements under various evolutionary models.
Conclusions:
- ProtParCon simplifies and accelerates the analysis of molecular evolution, specifically focusing on parallel and convergent amino acid substitutions.
- The package is freely available on GitHub and PyPI, promoting wider adoption in the research community.
- It serves as a valuable tool for researchers investigating adaptive evolution at the molecular level.
Related Concept Videos
03:42Amino acids
105.2K
Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible for...
105.2K
01:20Parallel Processing
703
The brain processes sensory information rapidly due to parallel processing, which involves sending data across multiple neural pathways at the same time. This method allows the brain to manage various sensory qualities, such as shapes, colors, movements, and locations, all concurrently. For instance, when observing a forest landscape, the brain simultaneously processes the movement of leaves, the shapes of trees, the depth between them, and the various shades of green. This enables a quick and...
703
01:18Amino Acid Catabolism
1.1K
Microorganisms rely on proteins as an essential carbon and energy source, particularly in environments with limited polysaccharides or lipids. However, proteins are too large to cross the plasma membrane unaided, necessitating enzymatic degradation. Microbes secrete extracellular proteases and peptidases that hydrolyze proteins into peptides, which can then be transported across the membrane. Once inside the cell, intracellular proteases degrade these peptides into free amino acids, which...
1.1K
01:29Amino Acid Biosynthetic Pathways
1.2K
Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
1.2K
01:54Convergent Evolution
32.8K
Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.
32.8K
03:05Acid Strength and Molecular Structure
33.0K
Binary Acids and Bases
In the absence of any leveling effect, the acid strength of binary compounds of hydrogen with nonmetals (A) increases as the H-A bond strength decreases down a group in the periodic table. For group 17, the order of increasing acidity is HF < HCl < HBr < HI. Likewise, for group 16, the order of increasing acid strength is H2O < H2S < H2Se < H2Te. Across a row in the periodic table, the acid strength of binary hydrogen compounds increases with increasing...
In the absence of any leveling effect, the acid strength of binary compounds of hydrogen with nonmetals (A) increases as the H-A bond strength decreases down a group in the periodic table. For group 17, the order of increasing acidity is HF < HCl < HBr < HI. Likewise, for group 16, the order of increasing acid strength is H2O < H2S < H2Se < H2Te. Across a row in the periodic table, the acid strength of binary hydrogen compounds increases with increasing...
33.0K