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NW-align specifications

Information


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

NW-align in publications

 (4)
PMCID: 5217627
PMID: 28056763
DOI: 10.1186/s12864-016-3400-0

[…] 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 […]

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

[…] sc-ec_percentsimilaritylongest, the 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_cai, ec_cbi, ec_fop, ec_sccai, ec_sccbi, ec_scfop, […]

PMCID: 5100048
PMID: 27604222
DOI: 10.1093/molbev/msw189

[…] 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., […]

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

[…] 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)., as described, hlig1, hssrp1, hppp1ca, and hppp1cc in entry clones were shuttled into the yeast destination vectors pag416gpd-ccdb-ha (ura3) and pag415gpd-ccdb-ha (leu2) to generate […]


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