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Subfields: Computational Biology & Bioinformatics

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Citations in the corpus

A tale of two clades: monkeypox viruses. (2005, methodology): “The predicted protein sequence alignments in Fig. 5 and Supplementary Fig. S1 (available in JGV Online) were constructed using CLUSTALW ( Higgins & Sharp, 1988 ).”
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization (2017, background): “The PartTree and DPPartTree options share a basic design, but the former uses k-mer-based distance to estimate the similarity between sequences [7], while the latter uses dynamic programming (DP) [8] to estimate the similarity.”
The PAS superfamily: sensors of environmental and developmental signals. (2000, methodology): “(A) Clustal alignment for the sequences corresponding to the PAS domains of mammalian family members (265).”
Multiple sequence alignment using partial order graphs (2002, background): “…sequences be aligned in 'the right order' (i.e. most similar sequences first), because there is no algorithmic guarantee that the overall alignment process will actually find an optimal alignment for any given sequence (Higgins and Sharp, 1988; Mevissen and Vingron, 1996; Notredame et al., 1998).”
The Four TCR Genes of Teleost Fish: The cDNA and Genomic DNA Analysis of Japanese Flounder (Paralichthys olivaceus) TCR α-, β-, γ-, and δ-Chains1 (2003, methodology): “The amino acid sequences of the four TCR C regions for all reported species were retrieved from GenBank, and aligned using the CLUSTALW program (29).”
Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees (2016, methodology): “A progressive method (Feng and Doolittle, 1987; Higgins and Sharp, 1988; Hogeweg and Hesper, 1984) with approximate guide trees.”
COFFEE: an objective function for multiple sequence alignments (1998, methodology): “6 (Thompson et al., 1994a), SAGA with the MSA objective function (SAGA-MSA) (Notredame and Higgins, 1996), PRRP (V 2.5.1), the iterative alignment method recently described by Gotoh (1996), PILEUP (Higgins and Sharp, 1988) in GCG v9.”
Are volatile unsaturated aldehydes from diatoms the main line of chemical defence against copepods (2002, methodology): “1.81 analysis (Higgins & Sharp 1988, Thompson et al. 1994).”
Classifying G-protein coupled receptors with support vector machines (2002, unknown): “’ for a semi-conservative substitution (Higgins and Sharp, 1988).”
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity (2013, methodology): “Several different methods, a rapid one based on the number of shared k-mers (15) and more rigorous ones based on local or global pairwise alignment scores (16–18), can be selected in this step, according to the data size.”