Pattern matching is a fundamental operation in
computational biology, information retrieval, and text processing.
Despite advances in algorithms, efficiently searching large-scale
texts, particularly genomic sequences spanning billions of base
pairs, remains a significant challenge. Existing approaches face
substantial limitations including Boyer-Moore algorithm’s poor
worst-case performance of O(mn) and limited scalability on large
datasets, KMP algorithm’s high memory overhead and poor
cache locality despite O(m+n) complexity, traditional suffix array
methods’ expensive O(mlogn) search time with costly preprocessing,
and hash-based approaches like Rabin-Karp’s vulnerability
to hash collisions and poor performance on repetitive sequences
common in genomic data.
This paper presents LCP-Optimized Suffix Array (LOSA),
a high-performance pattern matching algorithm that combines
suffix arrays with Longest Common Prefix (LCP) array optimizations
and parallel processing to achieve faster search times
with scalable memory usage. LOSA reduces the worst-case search
complexity from O(m log n) to nearly O(m + log n), where
m length pattern and n length the text. This improvement
is achieved through LCP-aware skips to minimize redundant
comparisons, as well as parallelized construction and query
phases, for modern multicore systems.

• The Identification of various mycobacterial species is critical for understanding their pathogenicity
  and epidemiology. Despite the existence of several established methods for identifying mycobacterial
  species, each of these methods has several significant limitations, including high costs, substantial
  time demands, and a restricted ability to detect a wide range of recoverable species. This study
  presents an in silico method using restriction fragment length polymorphism (RFLP) to differentially
  identify 75 clinically important mycobacterial species.The present investigation employed specific
  primer combinations to identify and generate a distinct hypervariable sequence across the ribosomal
  RNA gene. This unique sequence using appropriate restriction enzyme digestion followed by gel
  electrophoresis enabled the creation of highly precise and distinct patterns or profiles for each of the
  75 medically relevant Mycobacterium species, including members of closely related Mycobacterium
  complex groups. This approach can quickly and reliably identify mycobacterial species, allowing for
  more timely treatment decisions and contributing to beneficial epidemiological investigations.