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Related Experiment Video

Updated: Jun 2, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering

Kangseok Kim¹, Wonil Kim, Sunshin Kim

¹Department of Knowledge Information Security, Ajou University, Suwon, Korea.

Bioinformatics (Oxford, England)

|May 7, 2011

Summary

ReMark is a novel bioinformatics tool that automatically clusters orthologous proteins using combined Recursive and Markov Clustering (MCL) algorithms. This approach enhances the reliability and flexibility of ortholog detection across multiple genomes.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Orthologous proteins are crucial for understanding evolutionary relationships and functional conservation across species.
Accurate identification and clustering of orthologs are essential for comparative genomics and functional annotation.

Purpose of the Study:

To introduce ReMark, a fully automatic tool for clustering orthologs.
To enhance the reliability and flexibility of ortholog detection using a novel algorithmic approach.

Main Methods:

ReMark combines Recursive Clustering and Markov Clustering (MCL) algorithms.
It detects ortholog pairs via reciprocal BLAST best hits and recursively clusters them.
The MCL algorithm refines clusters using score matrices and an adjustable inflation factor.

Main Results:

ReMark utilizes diagonal scores for increased reliability in initial ortholog clustering.
The tool offers flexible ortholog clustering controlled by the MCL inflation factor.
Users can tailor orthologous protein clusters to specific research needs by adjusting the inflation factor.

Conclusions:

ReMark provides a robust and adaptable solution for automatic orthologous protein clustering.
The tool's adjustable inflation factor allows for customized ortholog grouping based on research objectives.
ReMark is freely available for non-commercial use on Windows and Linux platforms.