[
  {
    "id": "10.1007/978-981-16-9885-9_33",
    "type": "paper-conference",
    "title": "Efficient Structural Matching for RNA Secondary Structure Using Bit-Parallelism",
    "author": [
      {
        "family": "Muhammad",
        "given": "Muhammad Yusuf"
      },
      {
        "family": "Thandekkattu",
        "given": "Salu George"
      },
      {
        "family": "Rakshit",
        "given": "Sandip"
      },
      {
        "family": "Vajjhala",
        "given": "Narasimha Rao"
      }
    ],
    "editor": [
      {
        "literal": "Ch. Satyanarayana"
      },
      {
        "literal": "Debasis Samanta"
      },
      {
        "literal": "Xiao-Zhi Gao"
      },
      {
        "literal": "Rajiv Kumar Kapoor"
      }
    ],
    "container-title": "High Performance Computing and Networking: Select Proceedings of CHSN 2021",
    "collection-title": "Lecture Notes in Electrical Engineering",
    "issued": {
      "date-parts": [
        [
          2022,
          3,
          23
        ]
      ]
    },
    "volume": "853",
    "page": "399-409",
    "publisher": "Springer Nature Singapore",
    "ISSN": "1876-1100",
    "ISBN": "9789811698859",
    "DOI": "10.1007/978-981-16-9885-9_33",
    "URL": "https://www.narasimharao.net/research/rna-secondary-structure-matching-bit-parallelism/",
    "abstract": "The idea of matching parameters, complements, and constants symbols is referred to as structural matching or s-matching for short. In this paper, an efficient exact pattern matching bit-parallel algorithm is proposed to address RNA secondary structure queries using the concept of s-matching. This algorithm has good application in finding structural similarity between RNA sequences which could help in infer its biological function. We developed a new bit-parallel algorithm that can be implemented and advance the well-known shift-OR algorithm by adding a transformative approach of working with s-strings through coding techniques that were portable in the area of s-matching. Our algorithm advances for the exact s-matching problem on RNA secondary structure assumed to be optimal on average time. The proposed algorithm could help answer RNA matching queries, such as discovering precisely similar RNA and structurally similar RNA sequences, critical to the characterization of functional annotation of a newly discovered RNA.",
    "keyword": "Parallelism, Parameterized matching, Structural matching, Encoding, RNA, Algorithm, Sequences, RNA secondary structure, structural matching, s-matching, bit-parallel algorithms, Shift-Or algorithm, parameterized string matching, exact pattern matching, bioinformatics, sequence similarity, functional annotation",
    "language": "en"
  }
]