Rapid similarity searches of nucleic acid and protein data banks.
Open accessAbstract
With the development of large data banks of protein and nucleic acid sequences, the need for efficient methods of searching such banks for sequences similar to a given sequence has become evident. We present an algorithm for the global comparison of sequences based on matching k-tuples of sequence elements for a fixed k. The method results in substantial reduction in the time required to search a data bank when compared with prior techniques of similarity analysis, with minimal loss in sensitivity. The algorithm has also been adapted, in a separate implementation, to produce rigorous sequence alignments. Currently, using the DEC KL-10 system, we can compare all sequences in the entire Protein Data Bank of the National Biomedical Research Foundation with a 350-residue query sequence in less than 3 min and carry out a similar analysis with a 500-base query sequence against all eukaryotic sequences in the Los Alamos Nucleic Acid Data Base in less than 2 min.
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Needleman-Wunsch alignment of sequencing result with actual sequence showed 16 of 19 sites matched, indicating accuracy of 84.21%.
“To evaluate the sequencing accuracy, we used the Needleman-Wunsch alignment in DNAMAN software to compare the sequencing result with the actual sequence (46, 47). Sixteen of 19 sites were matched in the final alignment, which indicated that an accuracy of 84.21% was achieved.”
From Electrochemical DNA synthesis and sequencing on a single electrode with scalability for integrated data storage (2021) · cites this paper as [47]
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- Authors
- Wilbur, W. J., & Lipman, D. J.
- ORCID
- Lipman, D J
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 1983-02
- Volume
- 80
- Issue
- 3
- Pages
- 726-730
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC393452
- OpenAlex
- W1981014117
- Cited by
- 1,546
- References
- 11
- Citations by year
- 2026: 5 · 2025: 5 · 2024: 8 · 2023: 4 · 2022: 12 · 2021: 17 · 2020: 7 · 2019: 2 · 2018: 6 · 2017: 5 · 2016: 6 · 2015: 14 · 2014: 10 · 2013: 10 · 2012: 5
- FWCI
- 131.80
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- sequence similarity search, sequence comparison, protein sequence databases, sequence alignment, Protein Data Bank, search time reduction
- MeSH terms
- Amino Acid Sequence, Base Sequence, Computers, Nucleic Acids, Proteins
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