2015/06/08 by Yue Wang, Wang, Yue
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Chromosomal and Genetic Variations #Computational Engineering #Data Structures and Algorithms (cs.DS) #FOS: Biological sciences #FOS: Computer and information sciences #Finance #Genome Rearrangement Algorithms #Genomics (q-bio.GN) #RNA and protein synthesis mechanisms #and Science (cs.CE)
paper · pdf · doi:10.48550/arxiv.1506.02424
openalex publication_date 2015/06/08 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine transposons in given gene sequences. Through an intuitive rule, we transform the biological problem of determining transposons into a rigorous mathematical problem of determining the longest common subsequence. Depending on whether the gene sequence is linear (each sequence has a fixed head and tail) or circular (we can choose any gene as the head, and the previous one is the tail), and whether genes have multiple copies, we classify the problem of determining transposons into four scenarios: (1) linear sequences without duplicated genes; (2) circular sequences without duplicated genes; (3) linear sequences with duplicated genes; (4) circular sequences with duplicated genes. With the help of graph theory, we design fast algorithms for different scenarios. We also derive some results that might be of theoretical interests in combinatorics.