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NW-align specifications

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Unique identifier OMICS_03693
Name NW-align
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

NW-align citations

 (6)
library_books

Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles

2017
BMC Bioinformatics
PMCID: 5333177
DOI: 10.1186/s12859-016-1427-5

[…] a gene/protein under analysis and its nearest ortholog (from the closest species). Amino acid sequences are retrieved via KEGG REST API and then aligned using the Needleman–Wunsch algorithm [] using NW-align code (http://zhanglab.ccmb.med.umich.edu/NW-align/). The codon alignment is obtained using the protein alignment; Ka/Ks ratio is calculated using Java code from the program Ka/Ks calculator [ […]

library_books

Unsupervised statistical discovery of spaced motifs in prokaryotic genomes

2017
BMC Genomics
PMCID: 5217627
PMID: 28056763
DOI: 10.1186/s12864-016-3400-0

[…] t our goal is to discount all motif pairs which likely arose from recent duplication of the whole segment including the motif pair and the spacer. Consequently, sequence alignments are performed with NW-align, which is a simple and robust alignment program based on the standard Needleman-Wunsch algorithm [], to eliminate potential duplicated spacers. A simple ‘greedy’ algorithm is applied to elimi […]

library_books

Systematic bacterialization of yeast genes identifies a near universally swappable pathway

2017
eLife
PMCID: 5536947
PMID: 28661399
DOI: 10.7554/eLife.25093.026

[…] imilarityAlignedSc-Ec_PercentSimilarityLongestThe fraction of identical residues (PercentID) or similar residues (PercentSimilarity) in a global alignment (NWalign, http://zhanglab.ccmb.med.umich.edu/NW-align/) of the respective orthologs, as a function of the longest of the two (Longest) or the length of the aligned region (Aligned).Ec_CAIEc_CBIEc_FOPEc_ScCAIEc_ScCBIEc_ScFOPThe Codon Adaptation I […]

library_books

Evolutionary Dynamics of Abundant Stop Codon Readthrough

2016
Mol Biol Evol
PMCID: 5100048
PMID: 27604222
DOI: 10.1093/molbev/msw189

[…] op codon of each than there are for 98.9% of pairs in the null model that we constructed, as described below. Alignments were calculated using the Needleman–Wunsch dynamic programming protein aligner NW-align (). We made this relationship transitive by also considering two transcripts to have homologous final exons if both final exons are homologous to the final exon of some third transcript.The c […]

library_books

Complementation of Yeast Genes with Human Genes as an Experimental Platform for Functional Testing of Human Genetic Variants

2015
Genetics
PMCID: 4649650
PMID: 26354769
DOI: 10.1534/genetics.115.181099

[…] ulated using a Mann–Whitney test. For some manually curated orthologs and others generated from Yeastmine, sequence identity was determined using NWalign (Y. Zhang, http://zhanglab.ccmb.med.umich.edu/NW-align). […]

library_books

Ab Initio structure prediction for Escherichia coli: towards genome wide protein structure modeling and fold assignment

2013
Sci Rep
PMCID: 3667494
PMID: 23719418
DOI: 10.1038/srep01895

[…] sequence matches with multiple PDB chains, we choose the experimental structure which has the highest sequence identity to the target sequence, where the pair-wise sequence identity is calculated by NW-align (http://zhanglab.ccmb.med.umich.edu/NW-align). In total, 1,019 E. coli sequences have full or partial structures solved by experiments. Proteins which have structures covering less than half […]


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