Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

<i>Psychrobacillus syltrankelensis</i> sp. nov., a new species isolated from soil in the North Caucasus, Russia.

Microbiology spectrum·2026
Same author

Characterization of <i>Bacillus velezensis</i> EV17 and K-3618 and Their Polyketide Antibiotic Oxydifficidin, an Inhibitor of Prokaryotic Translation with Low Cytotoxicity.

International journal of molecular sciences·2025
Same author

<i>Bacillus</i>-Based Biocontrol Agents Mediate Pathogen Killing by Biodegradable Antimicrobials from Macrolactin Family.

International journal of molecular sciences·2025
Same author

Proposal of <i>Bacillus altaicus</i> sp. nov. Isolated from Soil in the Altai Region, Russia.

International journal of molecular sciences·2025
Same author

The bacterial OMP amyloids modulate α-synuclein and amyloid-β aggregation.

International journal of biological macromolecules·2025
Same author

Pathogenesis-Associated Bacterial Amyloids: The Network of Interactions.

Biochemistry. Biokhimiia·2025

Related Experiment Video

Updated: May 9, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

SARP: A Novel Algorithm to Assess Compositional Biases in Protein Sequences.

Kirill S Antonets1, Anton A Nizhnikov

  • 1Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.

Evolutionary Bioinformatics Online
|August 7, 2013
PubMed
Summary
This summary is machine-generated.

We developed Sequence Analysis based on the Ranking of Probabilities (SARP), a novel algorithm for detecting compositional biases in biological sequences. SARP offers high accuracy and is significantly faster than existing methods, ideal for large datasets.

Keywords:
algorithmcompositionprobabilityproteinsequence analysis

More Related Videos

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Related Experiment Videos

Last Updated: May 9, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Biological sequences (DNA, RNA, proteins) are defined by subunit composition (nucleotides, amino acids).
  • Compositional biases, local shifts in subunit frequencies, indicate organismal adaptation or protein function/localization.
  • Accurate detection of these biases is crucial for biological sequence analysis.

Purpose of the Study:

  • To introduce a novel algorithm, Sequence Analysis based on the Ranking of Probabilities (SARP), for annotating compositional biases.
  • To provide a computationally efficient method for identifying biased subsequences.

Main Methods:

  • Developed the SARP algorithm, which ranks subsequences based on their calculated probabilities.
  • Compared SARP's performance against the established Lower Probability Subsequences (LPS) algorithm.

Main Results:

  • SARP demonstrates comparable accuracy to the LPS algorithm in detecting compositional biases.
  • SARP achieves an approximately 230-fold increase in processing speed compared to LPS.
  • The algorithm is highly effective for analyzing large biological sequence datasets.

Conclusions:

  • SARP is a highly accurate and significantly faster alternative for compositional bias annotation.
  • The algorithm's efficiency makes it suitable for large-scale genomic and proteomic analyses.
  • SARP can reduce the computational time and resources required for sequence analysis.