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q-bio.GN2025
Minimum-Cost Synthetic Genome Planning: An Algorithmic Framework
Michail Patsakis, Ioannis Mouratidis, Ilias Georgakopoulos-Soares
As synthetic genomics scales toward the construction of increasingly larger genomes, computational strategies are needed to address technical feasibility. We introduce an algorithm…
q-bio.GN2024
MAFcounter: An efficient tool for counting the occurrences of k-mers in MAF files
Michail Patsakis, Kimonas Provatas, Ioannis Mouratidis +1
Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These al…
q-bio.GN2024
Zimin patterns in genomes
Nikol Chantzi, Ioannis Mouratidis, Ilias Georgakopoulos-Soares
Zimin words are words that have the same prefix and suffix. They are unavoidable patterns, with all sufficiently large strings encompassing them. Here, we examine for the first tim…