https://ioannis-mouratidis.github.io/tags/Bioinformatics/BioinformaticsHugo Blox Builder (https://hugoblox.com)en-usWed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/media/icon_hu_899445b689d8f445.pnghttps://ioannis-mouratidis.github.io/tags/Bioinformatics/https://ioannis-mouratidis.github.io/projects/zseeker/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/projects/zseeker/<h2 id="overview">Overview</h2> <p>Zseeker is an open-source Python tool designed for optimized detection of Z-DNA forming sequences in large genomic datasets. Z-DNA is an alternative left-handed DNA structure implicated in gene regulation, genome instability, and various biological processes.</p> <h2 id="features">Features</h2> <ul> <li><strong>High Performance</strong>: Optimized algorithms enable analysis of entire genomes</li> <li><strong>Accuracy</strong>: Improved detection accuracy compared to previous methods</li> <li><strong>Scalability</strong>: Designed to handle large-scale genomic datasets</li> <li><strong>Easy to Use</strong>: Simple Python interface with clear documentation</li> <li><strong>Open Source</strong>: Freely available for academic and commercial use</li> </ul> <h2 id="technical-details">Technical Details</h2> <p>Zseeker implements advanced algorithms for identifying sequences capable of forming Z-DNA structures based on sequence composition and thermodynamic properties. The tool is optimized for both speed and accuracy, making it suitable for genome-wide analyses.</p> <h2 id="use-cases">Use Cases</h2> <ul> <li>Genome-wide Z-DNA mapping</li> <li>Regulatory element identification</li> <li>Genome stability studies</li> <li>Comparative genomics of non-B DNA structures</li> <li>Disease-associated variant analysis</li> </ul> <h2 id="publications">Publications</h2> <p>Wang, G., Mouratidis, I., Provatas, K., et al. (2025). ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequences. <em>Briefings in Bioinformatics, 26</em>(3).</p>https://ioannis-mouratidis.github.io/publications/zseeker-2025/Wed, 01 Jan 2025 00:00:00 +0000https://ioannis-mouratidis.github.io/publications/zseeker-2025/<p>ZSeeker provides researchers with a fast and accurate tool for identifying Z-DNA forming sequences across entire genomes, facilitating studies of genome regulation and stability.</p>https://ioannis-mouratidis.github.io/projects/kmerdb/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/projects/kmerdb/<h2 id="overview">Overview</h2> <p>kmerDB is a comprehensive database that consolidates genomic and proteomic k-mer sequence information across all species in Genbank and UniProt. This resource enables rapid species identification, comparative genomic studies, and evolutionary analysis.</p> <h2 id="features">Features</h2> <ul> <li><strong>Comprehensive Coverage</strong>: Encompasses k-mer data from all species in major sequence databases</li> <li><strong>Dual Coverage</strong>: Includes both genomic (DNA) and proteomic (amino acid) sequences</li> <li><strong>Fast Queries</strong>: Optimized data structures enable rapid k-mer lookups</li> <li><strong>Species Identification</strong>: Enables efficient molecular diagnostics and species authentication</li> <li><strong>100-fold Compression</strong>: Novel compression procedures reduce data storage requirements dramatically</li> </ul> <h2 id="technical-implementation">Technical Implementation</h2> <p>The database was built using advanced compression algorithms achieving 100-fold data reduction while maintaining query performance. This enables storage and analysis of k-mer information from the entire tree of life.</p> <h2 id="applications">Applications</h2> <ul> <li>Species identification and authentication</li> <li>Comparative genomics</li> <li>Evolutionary studies</li> <li>Molecular diagnostics</li> <li>Environmental monitoring</li> <li>Food authentication</li> </ul> <h2 id="publications">Publications</h2> <p>Mouratidis, I., Baltoumas, F. A., Chantzi, N., et al. (2024). kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species. <em>Computational and Structural Biotechnology Journal, 23</em>.</p>https://ioannis-mouratidis.github.io/publications/kmerdb-2024/Mon, 01 Jan 2024 00:00:00 +0000https://ioannis-mouratidis.github.io/publications/kmerdb-2024/<p>kmerDB provides the research community with a powerful tool for k-mer based species identification, comparative genomics, and evolutionary studies.</p>