Identification of common molecular subsequences.

By Temple F. Smith, Michael S. Waterman. 1981

Subfields: Computational Biology & Bioinformatics

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In Computational Biology & Bioinformatics

Citations in the corpus

MLS: A Large-Scale Multilingual Dataset for Speech Research (2020, methodology): “We then perform a Smith-Waterman alignment [15] to ﬁnd the best matching sub-sequence of words.”
Evaluating Protein Transfer Learning with TAPE (2019, methodology): “Given a database of proteins and a new protein at test-time, an alignment-based method uses either carefully designed scoring systems to perform pairwise comparisons [21, 23], Hidden Markov Model-like probabilistic models [16], or a combination [13] to align the test protein against the database.”
Accelerated Profile HMM Searches (2011, neutral): “in ways comparable to how BLAST heuristically approximates and accelerates Smith/Waterman optimal dynamic programming alignment”
A Survey on Metric Learning for Feature Vectors and Structured Data (2013, methodology): “Similar metrics include the Needleman-Wunsch score (Needleman and Wunsch, 1970) and the Smith-Waterman score (Smith and Waterman, 1981).”
Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets (2011, methodology): “BLAST then extends and joins the seeds and refines them by a SmithWaterman alignment [32].”
Prediction of Human Activity by Discovering Temporal Sequence Patterns (2014, methodology): “(KNN or SVM kernel can be used as classifier in this scenario).”
PhyLAT: a phylogenetic local alignment tool (2012, methodology): “, 1997) and other accelerated variants of Smith–Waterman (Smith and Waterman, 1981) are widely used for pairwise sequence comparison, but these methods compare only individual sequences.”
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation (2011, methodology): “The recurrence relations for the algorithm of Smith and Waterman [1] with the modifications of Gotoh [2] for affine gap penalty functions are shown below.”
Sensitive protein alignments at tree-of-life scale using DIAMOND (2021, methodology): “The result of the chaining computation is used to infer a scaffold for the optimal alignment and to determine the band geometry for a banded Smith–Waterman algorithm 20 .”
A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation (2008, methodology): “The Smith/ Waterman alignment algorithm [44] is a unihit algorithm, for example, whereas BLAST is multihit, implementing ‘‘sum statistics’’ to allow multiple consistent hits to contribute to a target’s score [8].”
A brief survey on sequence classification (2010, methodology): “In contrast to global alignment algorithms, lo-cal alignment algorithms, such as the Smith-Waterman al-gorithm [53] and BLAST [6], measure the similarity between two sequences by considering the most similar regions but not enforcing the alignments on full length.”
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons (2011, methodology): “The algorithm generalizes the classical Smith-Waterman pairwise algorithm [28] so that the three reading frames are considered.”
Comparative Genomics (2007, unknown): “For instance, if 1 = 1 3 2 = 4 7 and = 1 4 2 3 5 7 6 , then 2 1 = 1 7 6 3 5 4 2 , a resulting permutation by exchanging blocks [4, 2] and [7, 6] in (1, 4, 2, 3, 5, 7, 6).”
Toward the solution of the protein structure prediction problem (2021, methodology): “Such algorithms include well-established methods developed in the 1970s and 1980s that utilize dynamic programming, such as the Needleman – Wunsch algo-rithm (85) for global alignment and the Smith – Waterman algorithm (86) for local alignment.”
YASS: enhancing the sensitivity of DNA similarity search (2005, methodology): “Except for small sequences, the exact local alignment algorithm of Smith and Waterman (1) is not frequently used, and most alignments are obtained using heuristic alignment tools such as FASTA (2), FLASH (3), BLAST (4,5), BLASTZ (6) and PatternHunter (7,8).”