4 papers
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…
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…
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…
MAFin: Motif Detection in Multiple Alignment Files
Michail Patsakis, Kimonas Provatas, Fotis A. Baltoumas +4
Motivation: Genome and Proteome Alignments, represented by the Multiple Alignment File (MAF) format, have become a standard approach in the field of comparative genomics and proteo…