Multiple Sequence Alignment Using ClustalW and ClustalX

By Julie Dawn Thompson, Toby J. Gibson, Desmond G. Higgins. 2003

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In Molecular Biology

Citations in the corpus

Unified rational protein engineering with sequence-based deep representation learning (2019, methodology): “Remaining sequences were then multiply aligned using ClustalW (gap open penalty = 10, gap extension penalty = 0.1) 78 .”
CEACAM1 regulates TIM–3–mediated tolerance and exhaustion (2014, positive): “In addition, multiple sequencealignmentswereperformedusingClustalW 45 .”
Batrachochytrium salamandrivorans sp. nov. causes lethal chytridiomycosis in amphibians (2013, background): “10 (24), and ambiguously aligned fragments were excluded for further analysis, resulting in a 1,513-bp reliably aligned data matrix.”
Immune epitope database analysis resource (2012, methodology): “The output page (Figure 2) provides mapping of the epitope to the source sequence, the PDB hits that contain the epitope regions, secondary structures and solvent accessibilities for each residue, presented in the format of either pairwise or multiple sequence alignment for the selected PDB hits, ob”
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud (2013, methodology): “The alignment is then used to construct a phylogenetic tree, using the EBI ClustalW phylogeny service.”
Pfam: the protein families database (2013, methodology): “In the Pfam website, we use two different colouring schemes when displaying our alignments in a web browser: the Clustal scheme (15), based on the chemical properties of the amino acids found in the column, and a heat-map scheme that reﬂects the posterior The seed alignment is used to construct the…”
Updating the 97% identity threshold for 16S ribosomal RNA OTUs (2017, background): “1 (Thompson et al., 2002) on 16S rRNA sequences from (Kozich et al., 2013).”
SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments (2016, methodology): “This alignment may have been generated by overlaying SNPs on a consensus reference genome, or using a multiple alignment tool, such as MUSCLE (Edgar, 2004), PRANK (Löytynoja, 2014), MAFFT (Katoh & Standley, 2013), or ClustalW (Thompson et al., 2002).”