2013/07/02 by Marius Nicolae, Nicolae, Marius, Sanguthevar Rajasekaran +1
Biochemistry, Genetics and Molecular Biology · Computer Science · #Algorithms and Data Compression #Computational Engineering #Data Structures and Algorithms (cs.DS) #FOS: Computer and information sciences #Finance #Genomics and Chromatin Dynamics #Genomics and Phylogenetic Studies #and Science (cs.CE) #cs.CE #cs.DS
paper · pdf · doi:10.48550/arxiv.1307.0571
arxiv created 2013/07/02 · openalex publication_date 2013/07/02 · arxiv updated 2013/07/03 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Motif searching is an important step in the detection of rare events occurring in a set of DNA or protein sequences. One formulation of the problem is known as (l,d)-motif search or Planted Motif Search (PMS). In PMS we are given two integers l and d and n biological sequences. We want to find all sequences of length l that appear in each of the input sequences with at most d mismatches. The PMS problem is NP-complete. PMS algorithms are typically evaluated on certain instances considered challenging. This paper presents an exact parallel PMS algorithm called PMS8. PMS8 is the first algorithm to solve the challenging (l,d) instances (25,10) and (26,11). PMS8 is also efficient on instances with larger l and d such as (50,21). This paper also introduces necessary and sufficient conditions for 3 l-mers to have a common d-neighbor.