Current Protocols in Bioinformatics This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.
This article describes the various options available to researchers and bioinformaticians who would like to use our resources via the web interface employing RESTful web service clients provided in Perl, Python, and Java, or would like to use Docker containers to integrate the resources into analysis pipelines and workflows. © 2019 by John Wiley & Sons, Inc. PMID: 31039604 [PubMed - as supplied by publisher] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - May 2, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks.
Authors: Rioualen C, Charbonnier-Khamvongsa L, Collado-Vides J, van Helden J Abstract Next-generation sequencing (NGS) is becoming a routine approach in most domains of the life sciences. To ensure reproducibility of results, there is a crucial need to improve the automation of NGS data processing and enable forthcoming studies relying on big datasets. Although user-friendly interfaces now exist, there remains a strong need for accessible solutions that allow experimental biologists to analyze and explore their results in an autonomous and flexible way. The protocols here describe a modular system that ena...
Source: Current Protocols in Bioinformatics - February 21, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Utilizing iVariantGuide for Variant Assessment of Next-Generation Sequencing.
Authors: Chaudhry SR, Tainsky MA Abstract Molecular genetic testing provides the capability for personalized prediction, diagnosis, and pharmacological treatments of disease and disorders. Variant assessment of next-generation sequencing (NGS) is a crucial component of genetic testing for clinicians to counsel patients on risk and management. The iVariantGuide application is a dynamic Web-based application made for the tertiary analysis of NGS. Along with variant assessment, iVariantGuide provides a unique interactive pathway impact analysis of genetic variants, as well as a unique Gene Ontology (GO) analy...
Source: Current Protocols in Bioinformatics - February 14, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle.
Authors: Tay AP, Liang A, Wilkins MR, Pang CNI Abstract Post-translational modifications (PTMs) of proteins act as key regulators of protein activity, including the regulation of protein-protein interactions (PPIs). However, exploring functional links between PTMs and PPIs can be difficult. PTMOracle is a Cytoscape app that facilitates the co-visualization and co-analysis of PTMs in the context of PPI networks. PTMOracle also allows extensive data to be integrated and co-analyzed, allowing the role of domains, motifs, and disordered regions to be considered. Here, we describe several PTMOracle protocols in...
Source: Current Protocols in Bioinformatics - January 19, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Discovering Transcriptional Regulatory Elements From Run-On and Sequencing Data Using the Web-Based dREG Gateway.
Authors: Chu T, Wang Z, Chou SP, Danko CG Abstract Transcription is a chromatin mark that can be used effectively to identify the location of active enhancers and promoters, collectively known as transcriptional regulatory elements (TREs). We recently introduced dREG, a tool for the identification of TREs using run-on and sequencing (RO-seq) assays, including global run-on and sequencing (GRO-seq), precision run-on and sequencing (PRO-seq), and chromatin run-on and sequencing (ChRO-seq). In this protocol, we present step-by-step instructions for running dREG on an arbitrary run-on and sequencing dataset. U...
Source: Current Protocols in Bioinformatics - December 29, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using OmicsNet for Network Integration and 3D Visualization.
This article contains three basic protocols covering the key features of OmicsNet, including how to create biological networks from a single or multiple list(s) of molecules, how to integrate or enrich different types of networks, and how to navigate the 3D visualization system to obtain biological insights. The OmicsNet web server is freely available at https://www.omicsnet.ca. © 2018 by John Wiley & Sons, Inc. PMID: 30556956 [PubMed - as supplied by publisher] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - December 19, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using the sORFs.Org Database.
Authors: Olexiouk V, Menschaert G Abstract Ribosome profiling involves sequencing of approximately 30-base-long stretches of ribosome-protected mRNA. The technique enables genome-wide mapping of RNA undergoing active translation. Numerous small open reading frames have been identified by using ribosome profiling, leading researchers to question the assumed non-functional character of sORFs and to the identification of various important sORF translation products. sORFs.org (https://www.sorfs.org) is a public repository of small open reading frames identified by ribosome profiling in a database of over 3 mil...
Source: Current Protocols in Bioinformatics - November 30, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Identification of Key Residues in Proteins Through Centrality Analysis and Flexibility Prediction with RINspector.
Authors: Brysbaert G, Mauri T, de Ruyck J, Lensink MF Abstract Protein structures inherently contain information that can be used to decipher their functions, but the exploitation of this knowledge is not trivial. We recently developed an app for the Cytoscape network visualization and analysis program, called RINspector, the goal of which is to integrate two different approaches that identify key residues in a protein structure or complex. The first approach consists of calculating centralities on a residue interaction network (RIN) generated from the three-dimensional structure; the second consists of pr...
Source: Current Protocols in Bioinformatics - November 30, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Predicting Genes in Single Genomes with AUGUSTUS.
Authors: Hoff KJ, Stanke M Abstract AUGUSTUS is a tool for finding protein-coding genes and their exon-intron structure in genomic sequences. It does not necessarily require additional experimental input, as it can be applied in so-called ab initio mode. However, extrinsic evidence from various sources such as transcriptome sequencing or the annotations of closely related genomes can be integrated in order to improve the accuracy and completeness of the annotation. AUGUSTUS can be applied to single genomes, or simultaneously to several aligned genomes. Here, we describe steps required for training AUGUSTUS...
Source: Current Protocols in Bioinformatics - November 23, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Good Citizenship Made Easy: A Step-by-Step Guide to Submitting RNA-Seq Data to NCBI.
Authors: Feindt W, Oppenheim SJ, DeSalle R, Mehr S Abstract The analysis of transcriptome data from non-model organisms contributes to our understanding of diverse aspects of evolutionary biology, including developmental processes, speciation, adaptation, and extinction. Underlying this diversity is one shared feature, the generation of enormous amounts of sequence data. Data availability requirements in most journals oblige researchers to make their raw transcriptome data publicly available, and the databases housed at the National Center for Biotechnology Information (NCBI) are a popular choice for data ...
Source: Current Protocols in Bioinformatics - November 15, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Pre-Processing MALDI/TOF Mass Spectra by Using Geena 2.
Authors: Romano P, Profumo A, Facchiano A Abstract Geena 2 is a tool for filtering, averaging, and aligning MALDI/TOF mass spectra, designed to assist scientists in the analysis of high volumes of data and support them for comparative studies. Three web interfaces are available with different levels of complexity. In this manuscript, we explain how to use Geena 2 with these three interfaces to perform analyses of one's own data. Two support protocols showing how to check the example input file and how to create an input file with own data are also presented. © 2018 by John Wiley & Sons, Inc. P...
Source: Current Protocols in Bioinformatics - November 15, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Investigation of RNA-RNA Interactions Using The RISE Database.
This article introduces RISE, a database of the RNA Interactome from Sequencing Experiments. RISE provides a comprehensive collection of RRIs in human, mouse, and yeast, derived from transcriptome-wide sequencing experiments, as well as targeted sequencing studies and other public databases/datasets. To facilitate better understanding of the biological roles of these RRIs, RISE also offers rich functional annotations involving RNAs, and an interactive interface to explore the analysis results. Here, we provide a brief description of the RISE website and a step-by-step protocol for using RISE to study RRIs. © 2018 by John ...
Source: Current Protocols in Bioinformatics - November 9, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using geneid to Identify Genes.
Authors: Alioto T, Blanco E, Parra G, Guigó R Abstract This unit describes the usage of geneid, an efficient gene-finding program that allows for the analysis of large genomic sequences, including whole mammalian chromosomes. These sequences can be partially annotated, and geneid can be used to refine this initial annotation. Training geneid is relatively easy, and parameter configurations exist for a number of eukaryotic species. geneid produces output in a variety of standard formats. The results, thus, can be processed by a variety of software tools, including visualization programs. geneid software is...
Source: Current Protocols in Bioinformatics - October 19, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure.
Authors: Chougule KM, Wang L, Stein JC, Wang X, Devisetty UK, Klein RR, Ware D Abstract RNA-seq is a vital method for understanding gene structure and expression patterns. Typical RNA-seq analysis protocols use sequencing reads of length 50 to 150 nucleotides for alignment to the reference genome and assembly of transcripts. The resultant transcripts are quantified and used for differential expression and visualization. Existing tools and protocols for RNA-seq are vast and diverse; given their differences in performance, it is critical to select an analysis protocol that is scalable, accurate, and easy to ...
Source: Current Protocols in Bioinformatics - September 2, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Analysis and Visualization of Dynamic Networks Using the DyNet App for Cytoscape.
Authors: Salamon J, Goenawan IH, Lynn DJ Abstract Biological processes are regulated at a cellular level by tightly controlled molecular interaction networks, which are collectively known as the interactome. The interactome is not a static entity, but instead is dynamically reorganized or "rewired" under varying temporal, spatial, and environmental conditions. Most network analysis and visualization tools have, to date, been developed for static representations of molecular interaction data. Here, we describe a protocol that provides a step-by-step guide to DyNet, a Cytoscape 3 application that facilitates...
Source: Current Protocols in Bioinformatics - September 2, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research