The Feature-Viewer: a visualization tool for positional annotations on a sequence

Paladin, Lisanna; Schaeffer, Mathieu; Gaudet, Pascale; Zahn-Zabal, Monique; Michel, Pierre-André; Piovesan, Damiano; Tosatto, Silvio C. E.; Bairoch, Amos Marc

doi:10.1093/bioinformatics/btaa055

Cited by 24 publications

(21 citation statements)

References 9 publications

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“…The user interface was developed in javascript using bootstrap version 3.3.7, jquery version 3.1.1 and datatables version 1.10.11. The feature visualisation panel uses the neXtProt feature viewer package version 0.1.44 39 . The website is hosted at http://134.36.66.166:8070/home .…”

Section: Methodsmentioning

confidence: 99%

Visualisation of experimentally determined and predicted protein N-glycosylation and predicted glycosylphosphatidylinositol anchor addition in Trypanosoma brucei.

Tinti

Ferguson

2022

Wellcome Open Res

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Background: Trypanosoma brucei is a protozoan parasite and the etiological agent of human and animal African trypanosomiasis. The organism cycles between its mammalian host and tsetse vector. The host-dwelling bloodstream form of the parasite is covered with a monolayer of variant surface glycoprotein (VSG) that enables it to escape both the innate and adaptive immune systems. Within this coat reside lower-abundance surface glycoproteins that function as receptors and/or nutrient transporters. The glycosylation of the Trypanosoma brucei surface proteome is essential to evade the immune response and is mediated by three oligosaccharyltransferase genes; two of which, TbSTT3A and TbSTT3B, are expressed in the bloodstream form of the parasite. Methods: We processed a recent dataset of our laboratory to visualise putative glycosylation sites of the Trypanosoma brucei proteome. We provided a visualisation for the predictions of glycosylation carried by TbSTT3A and TbSTT3B, and we augmented the visualisation with predictions for Glycosylphosphatidylinositol anchoring sites, domains and topology of the Trypanosoma brucei proteome. Conclusions: We created a web service to explore the glycosylation sites of the Trypanosoma brucei oligosaccharyltransferases substrates, using data described in a recent publication of our laboratory. We also made a machine learning algorithm available as a web service, described in our recent publication, to distinguish between TbSTT3A and TbSTT3B substrates.

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Section: Methodsmentioning

confidence: 99%

Visualisation of experimentally determined and predicted protein N-glycosylation and predicted glycosylphosphatidylinositol anchor addition in Trypanosoma brucei.

Tinti

Ferguson

2022

Wellcome Open Res

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“…Mutation Maker is composed of five distinct components as follows: (i) A JavaScript (JS) User Interface (UI) where users can submit oligo design tasks and visualize the results using a customized version of the neXtProt viewer (Paladin et al, 2020; Zahn-Zabal et al, 2019), (ii) A Worker that is assigned by the open source Celery asynchronous task queue, where computation takes place, (iii) An Application Programming Interfaces (API) that provide communication between the UI and the Worker, (iv) An open source Redis in-memory database that is used to temporarily store information about the design task and its respective results, (v) The AWS (Amazon Web Services) Lambda service is also optionally employed to parallelize part of the SSSM computation that utilizes Primer3 binary (Rozen and Skaletsky, 2000; Untergasser et al, 2012). However, Mutation Maker can run on any computer that provides 256MB RAM for the UI, 512MB RAM for the API, and 8GB RAM for the Worker.…”

Section: Methodsmentioning

confidence: 99%

“…Each workflow consists of an input form with advanced on-the-go validation and a dynamic result page. Results are displayed using interactive table, modified neXtProt Feature Viewer (Paladin et al, 2020; Zahn-Zabal et al, 2019) and Excel export. Results with input parameters can be exported to PDF or as a temporary sharable link.…”

Section: Methodsmentioning

confidence: 99%

“…Designed oligos can be exported as annotated XLSX file. The neXtProt Feature Viewer is JavaScript Library developed by Swiss Institute of Bioinformatics (SIB) to visualize protein sequence features using D3 design (Paladin et al, 2020; Zahn-Zabal et al, 2019). These libraries have been modified to meet the visualization requirements for our three design workflows.…”

Section: Methodsmentioning

confidence: 99%

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Mutation Maker, An Open Source Oligo Design Platform for Protein Engineering

Hiraga

Mejzlík²,

Marcisin³

et al. 2020

Preprint

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Founded on principles of natural selection, directed evolution techniques harness high-throughput gene diversification methodologies to generate proteins with optimized properties for applications in research, therapeutic and industrial processes. However, design of gene libraries is typically hampered by scale and complexity, necessitating development of advanced automation and optimization tools that can improve efficiency and accuracy. At present, automated library design tools are obsolete, functionally limited or not freely available for commercial use. To address these issues, we developed Mutation Maker, an open source mutagenic oligo design software for large-scale protein engineering experiments. Mutation Maker is not only specifically tailored to multi-site random and directed mutagenesis protocols, but also pioneers bespoke mutagenic oligo design for de novo gene synthesis workflows. Enabled by a novel bundle of orchestrated heuristics, optimization, constraint-satisfaction and backtracking algorithms, Mutation Maker offers a versatile toolbox for gene diversification design at industrial scale. Supported by in-silico simulations and compelling experimental validation data, Mutation Maker oligos produce diverse gene libraries at high success rates irrespective of genes or vectors used. Finally, Mutation Maker was created as an extensible platform on the notion that directed evolution techniques will continue to evolve and revolutionize current and future-oriented applications.

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“…The rest of the Entry page provides a graphical view of structural features of the ensemble. The Feature-Viewer ( 56 ) component summarizes the make-up at the chain level. It shows the protein construct, solvent accessibility, secondary-structure populations and the respective variability (entropy or standard deviation) across ensemble models.…”

Section: Novel Featuresmentioning

confidence: 99%

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins

Lázár

Martínez‐Pérez

Quaglia

et al. 2020

Nucleic Acids Research

Self Cite

119

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The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.

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The Feature-Viewer: a visualization tool for positional annotations on a sequence

Cited by 24 publications

References 9 publications

Visualisation of experimentally determined and predicted protein N-glycosylation and predicted glycosylphosphatidylinositol anchor addition in Trypanosoma brucei.

Visualisation of experimentally determined and predicted protein N-glycosylation and predicted glycosylphosphatidylinositol anchor addition in Trypanosoma brucei.

Mutation Maker, An Open Source Oligo Design Platform for Protein Engineering

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins

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