A general method applicable to the search for similarities in the amino acid sequence of two proteins.

By S. B. Needleman, C. D. Wunsch. 1970

Subfields: Computational Biology & Bioinformatics

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Biology & Bioinformatics

Citations in the corpus

Sampling alternative conformational states of transporters and receptors with AlphaFold2 (2022, neutral): “The following templates were used: OF MCT1 with FucB (PDB 3O7Pa and 3O7Qa, 18% sequence identity calculated using Needleman Wunsch Needleman and Wunsch, 1970 ; Madeira et al., 2019 ); OF LAT1 with AdiC (3OB6a and 5J4Ib, 22%); IF LAT1 with b(0,+)AT1 (6LI9, 45%), KCC3 (6Y5Ra, 12%), GkApcT (6F34a,…”
ProGen: Language Modeling for Protein Generation (2020, methodology): “This score is based on the Needleman-Wunsch algorithm (Needleman & Wunsch, 1970) informed by the BLOSUM62 substitution matrix.”
Learning protein sequence embeddings using information from structure (2019, neutral): “These methods are either direct sequence alignment tools [31, 32] or based on profile HMMs in which multiple sequence alignments are first built by iterative search against a large sequence database, the multiple sequence alignments are converted into profile HMMs, and then sequences are compared us”
TM-align: a protein structure alignment algorithm based on the TM-score (2005, neutral): “In STRUCTAL (14) and SAL (18), the authors used the inter-structural residue–residue distance based LGscore matrix and maximized the cumulative LG-score (14) or relative RMSD (12) by a heuristic iteration of Needleman– Wunsch dynamic program (19).”
LOMETS: A local meta-threading-server for protein structure prediction (2007, neutral): “Dynamic programming algorithm (20) is used to find the best sequence–structure match.”
BALBES: a molecular-replacement pipeline (2007, methodology): “All entries in the database (around 14 000 subunits) were aligned with each other using a modified version of the Needleman & Wunsch (1970) dynamic alignment algorithm.”
The Tangled Web of Password Reuse (2014, unknown): “• Alignment-like functions : Smith-Waterman [45], Neddleman Wunsch [40], Largest Common Subse-quence (LCS) .”
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (2008, unknown): “The situation would be similar to that of a pure sequence alignment problem, for which the optimum solution is exactly calculated by using a two-dimensional dynamic programming (DP) algorithm [16,17] in cases with two sequences.”
ScanMatch: A novel method for comparing fixation sequences (2010, methodology): “The methods developed in this area range from robust and accurate but slow, such as the Needleman–Wunsch algorithm ( Needleman & Wunsch, 1970 ), to very fast but without the guarantee of finding the optimal solution, such as the BLAST algorithm (Altschul”
MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information (2008, unknown): “Because we use dynamics programming (DP)38,39 to search the alignment space, we only consider the single-body features which can be conveniently exploited in DP.”
Fast overlapping of protein contact maps by alignment of eigenvectors (2010, unknown): “Our approach uses standard techniques such as the canonical eigendecomposition of symmetric matrices (Strang, 2003) and the Needleman–Wunsch (NW) alignment algorithm (Needleman and Wunsch, 1970).”
A benchmark of multiple sequence alignment programs upon structural RNAs (2005, background): “This can be performed by aligning sequences globally [34] or locally [35], both employ dynamic programming, thus resulting in a quadratic time complexity.”
Database resources of the National Center for Biotechnology Information (2006, unknown): “Splign uses a version of the Needleman–Wunsch algorithm (26) that accounts for splice signals in combination with BLAST to identify possible locations of genes and their copies as well as to speed up the core dynamic programming.”
RotaC: A web-based tool for the complete genome classification of group A rotaviruses (2009, unknown): “In a second step, a distance matrix, based on pairwise alignments with the Needleman-Wunsch algorithm [8], and a phylogenetic tree based on the neighbor-joining algorithm using the Paup* software [9] are constructed and analyzed to identify the genotype of the query sequence by using the nucleotide ”
A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies (2009, unknown): “My implementation of the Needleman-Wunsch algorithm aligned between 21 and 73 sequences per second.”