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Protein Sequence Analysis Using the MPI Bioinformatics Toolkit.
Authors: Gabler F, Nam SZ, Till S, Mirdita M, Steinegger M, Söding J, Lupas AN, Alva V Abstract The MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) provides interactive access to a wide range of the best-performing bioinformatics tools and databases, including the state-of-the-art protein sequence comparison methods HHblits and HHpred. The Toolkit currently includes 35 external and in-house tools, covering functionalities such as sequence similarity searching, prediction of sequence features, and sequence classification. Due to this breadth of functionality, the tight interconnection of its ...
Source: Current Protocols in Bioinformatics - December 15, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt.
We describe how to search DisProt annotations, using both the web interface and the API for programmatic access. Finally, we explain how to visualize and interpret a DisProt entry, p53, a widely studied protein characterized by the presence of unstructured N-terminal and C-terminal regions. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Performing a search in DisProt Support Protocol 1: Downloading options Support Protocol 2: Programmatic access with DisProt REST API Basic Protocol 2: Visualizing and interpreting DisProt entries: the p53 use case Basic Protocol 3: Providing feedback and submitting new intrinsic disorder-...
Source: Current Protocols in Bioinformatics - October 6, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Network Building with the Cytoscape BioGateway App Explained in Five Use Cases.
Authors: Puig RR, Holmås S, Mironov V, Kuiper M Abstract The BioGateway App is a plugin for the Cytoscape network editor, allowing users to interactively build biological networks by querying the Biogateway Resource Description Framework (RDF) triple store. BioGateway contains information from several curated resources including UniProtKB, IntAct, Gene Ontology Annotations, various datasets containing transcription-factor regulatory relations to specific target genes, and more. The BioGateway App facilitates the step-by-step creation of complex SPARQL queries through an intuitive Graphical User Interface,...
Source: Current Protocols in Bioinformatics - September 30, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Expanding the Perseus Software for Omics Data Analysis With Custom Plugins.
Authors: Yu SH, Ferretti D, Schessner JP, Rudolph JD, Borner GHH, Cox J Abstract The Perseus software provides a comprehensive framework for the statistical analysis of large-scale quantitative proteomics data, also in combination with other omics dimensions. Rapid developments in proteomics technology and the ever-growing diversity of biological studies increasingly require the flexibility to incorporate computational methods designed by the user. Here, we present the new functionality of Perseus to integrate self-made plugins written in C#, R, or Python. The user-written codes will be fully integrated in...
Source: Current Protocols in Bioinformatics - September 17, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Exploring Non-Coding RNAs in RNAcentral.
This article describes different ways of accessing the data, including searching the website and retrieving the data programmatically over web APIs and a public database. We also demonstrate an example Galaxy workflow for using RNAcentral for RNA-seq differential expression analysis. RNAcentral is available at https://rnacentral.org. © 2020 The Authors. Basic Protocol 1: Viewing RNAcentral sequence reports Basic Protocol 2: Using RNAcentral text search to explore ncRNA sequences Basic Protocol 3: Using RNAcentral sequence search Basic Protocol 4: Using RNAcentral FTP archive Support Protocol 1: Using web APIs for programm...
Source: Current Protocols in Bioinformatics - August 29, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource.
Authors: Brunet MA, Lekehal AM, Roucou X Abstract Ten of thousands of open reading frames (ORFs) are hidden within genomes. These alternative ORFs, or small ORFs, have eluded annotations because they are either small or within unsuspected locations. They are found in untranslated regions or overlap a known coding sequence in messenger RNA and anywhere in a "non-coding" RNA. Serendipitous discoveries have highlighted these ORFs' importance in biological functions and pathways. With their discovery came the need for deeper ORF annotation and large-scale mining of public repositories to gather supporting expe...
Source: Current Protocols in Bioinformatics - August 13, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using SPAdes De Novo Assembler.
Authors: Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A Abstract SPAdes-St. Petersburg genome Assembler-was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single-cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and tr...
Source: Current Protocols in Bioinformatics - June 21, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

iSwathX 2.0 for Processing DDA Spectral Libraries for DIA Data Analysis.
Authors: Noor Z, Mohamedali A, Ranganathan S Abstract The iSwathX web application processes and normalizes mass spectrometry-based proteomics spectral libraries generated in the data-dependent acquisition (DDA) approach. These libraries are stored in various proteomics repositories such as PeptideAtlas and NIST, or are user-generated and provide reference data for data-independent acquisition (DIA) targeted data extraction and analysis. iSwathX 2.0 can efficiently normalize DDA data from different instruments, gathered at different instances, and make it compatible with specific DIA experiments. Novel func...
Source: Current Protocols in Bioinformatics - June 3, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.
Authors: Estaki M, Jiang L, Bokulich NA, McDonald D, González A, Kosciolek T, Martino C, Zhu Q, Birmingham A, Vázquez-Baeza Y, Dillon MR, Bolyen E, Caporaso JG, Knight R Abstract QIIME 2 is a completely re-engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open-source web-based platform, to re-use available data for meta-analysis. The following basic proto...
Source: Current Protocols in Bioinformatics - April 29, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Analyzing Protein Disorder with IUPred2A.
Authors: Erdős G, Dosztányi Z Abstract IUPred2A is a combined prediction tool designed to discover intrinsically disordered or conditionally disordered proteins and protein regions. Intrinsically disordered regions exist without a well-defined three-dimensional structure in isolation but carry out important biological functions. Over the years, various prediction methods have been developed to characterize disordered regions. The existence of disordered segments can also be dependent on different factors such as binding partners or environmental traits like pH or redox potential, and recognizing such reg...
Source: Current Protocols in Bioinformatics - April 4, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

MetaBridge: An Integrative Multi-Omics Tool for Metabolite-Enzyme Mapping.
Authors: Blimkie T, Lee AH, Hancock REW Abstract MetaBridge is a web-based tool designed to facilitate the integration of metabolomics with other "omics" data types such as transcriptomics and proteomics. It uses data from the MetaCyc metabolic pathway database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) to map metabolite compounds to directly interacting upstream or downstream enzymes in enzymatic reactions and metabolic pathways. The resulting list of enzymes can then be integrated with transcriptomics or proteomics data via protein-protein interaction networks to perform integrative multi-omi...
Source: Current Protocols in Bioinformatics - March 23, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using ggtree to Visualize Data on Tree-Like Structures.
This article contains five basic protocols describing how to visualize trees using the grammar of graphics syntax, how to visualize hierarchical clustering results with associated data, how to estimate bootstrap values and visualize the values on the tree, how to estimate continuous and discrete ancestral traits and visualize ancestral states on the tree, and how to visualize a multiple sequence alignment with a phylogenetic tree. The ggtree package is freely available at https://www.bioconductor.org/packages/ggtree. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Using grammar of graphics for visualizing trees Ba...
Source: Current Protocols in Bioinformatics - March 13, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Visualizing Human Protein-Protein Interactions and Subcellular Localizations on Cell Images Through CellMap.
Authors: Dallago C, Goldberg T, Andrade-Navarro MA, Alanis-Lobato G, Rost B Abstract Visualizing protein data remains a challenging and stimulating task. Useful and intuitive visualization tools may help advance biomolecular and medical research; unintuitive tools may bar important breakthroughs. This protocol describes two use cases for the CellMap (http://cellmap.protein.properties) web tool. The tool allows researchers to visualize human protein-protein interaction data constrained by protein subcellular localizations. In the simplest form, proteins are visualized on cell images that also show protein-p...
Source: Current Protocols in Bioinformatics - March 10, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Mothulity Facilitates 16S/ITS Amplicon Diversity Analysis.
We present Mothulity-a novel interface for Mothur, a well-established tool for 16S/ITS biodiversity analysis. Although Mothur is a well-documented and virtually complete software suite, its proper execution might be challenging for first-time users, and editing the Mothur batch scripts is time consuming even for experienced users. Mothur produces little to no graphical output, leaving the generation of plots to the user. Mothulity minimizes the chance of human error through a minimalistic yet powerful interface, with most of the analysis parameters predefined or adjusted automatically. Time spent on running the analysis is...
Source: Current Protocols in Bioinformatics - February 25, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Constructing and Analyzing Computational Models of Cell Signaling with BioModelAnalyzer.
Authors: Hall BA, Fisher J Abstract BioModelAnalyzer (BMA) is an open-source graphical tool for the development of executable models of protein and gene networks within cells. Based upon the Qualitative Networks formalism, the user can rapidly construct large networks, either manually or by connecting motifs selected from a built-in library. After the appropriate functions for each variable are defined, the user has access to three analysis engines to test the model. In addition to standard simulation tools, BMA includes an interface to the stability-testing algorithm and to a graphical Linear Temporal Log...
Source: Current Protocols in Bioinformatics - February 22, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research