BIOINFORMATICS APPLICATIONS NOTE

By Sequence analysis

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Citations in the corpus

Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2 (2013, neutral): “Clicking on the link at the bottom of the alignment panel opens the Jalview (Waterhouse et al., 2009) alignment viewer applet with the complete multiple alignment loaded.”
JPred4: a protein secondary structure prediction server (2015, neutral): “For users who have local installations of Jalview (36), Jalview feature files are provided to allow easy annotation and analysis of the alignment and predictions.”
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations (2010, unknown): “Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ: Jalview Version 2–a multiple sequence alignment editor and analysis workbench.”
Ribose 2′-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5 (2011, unknown): “Amino acids were assigned colors according the conventions of ClustalX for amino acid similarity and conservation as implemented in the JalView alignment editor 45 .”
Computational pan-genomics: status, promises and challenges (2016, unknown): “At the base level such inclusive displays are somewhat analogous to popular MSA displays such as Mauve [150] or Jalview [151] that focus on displaying all the differences between a set of sequences as clearly as possible.”
Moyamoya disease factor RNF213 is a giant E3 ligase with a dynein-like core and a distinct ubiquitin-transfer mechanism (2020, unknown): “1), Xenopus laevis (Uniprot: tr|A0A1L8ETH7), Danio rerio (Uniprot: sp|A0A0R4IBK5); sequences were aligned with MAFFT version 7.427 (27), and visualized with Jalview26.”
QuasR: quantification and annotation of short reads in R (2014, methodology): “…data processing and biological interpretation, such as an efficient framework for working with genomic ranges (Lawrence et al., 2013), or tools for read alignment (Liao et al., 2013), quality control (Morgan et al., 2009) and statistical analysis (Anders and Huber 2010; Robinson et al., 2010).”
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation (2021, unknown): “Tools, such as Jalview (45) or ProViz (46) can visualize sequence alignment and also show disorder information for a single protein, but they cannot provide information on the evolutionary conservation of IDPs.”
Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors (2018, unknown): “Structural modeling and sequence alignments Sequence alignments were performed using Jalview software (UK) (39) using a percentage”
Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, background): “However, often these alignments can be verified manually and improved using for instances sequence alignment editors like JalView (87).”
Influenza Research Database: An integrated bioinformatics resource for influenza research and surveillance (2012, methodology): “Visualization of sequence alignments in IRD is based on the Java alignment editor JalView 44 (Figure 4).”
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data (2010, background): “…packages such as Ringo [21] and ACME [22], other fast moving deep-sequencing analysis capabilities and infrastructure (Table 1) such as ShortRead [23], DEGseq [24], edgeR [25], BayesPeak [26], chipseq, ChIP-seqR, Rolexa [27], BSgenome, IRanges, Biostrings, rtrack-layer [28], GenomeGraphs [29]…”