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Current Protocols in Bioinformatics

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https://read.qxmd.com/read/30747482/utilizing-ivariantguide-for-variant-assessment-of-next-generation-sequencing
#1
Sophia R Chaudhry, Michael A Tainsky
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) analysis...
February 12, 2019: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30653846/visualizing-post-translational-modifications-in-protein-interaction-networks-using-ptmoracle
#2
Aidan P Tay, Angelita Liang, Marc R Wilkins, Chi Nam Ignatius Pang
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 investigating complex PTM-associated relationships and their role in PPIs...
January 17, 2019: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30589513/discovering-transcriptional-regulatory-elements-from-run-on-and-sequencing-data-using-the-web-based-dreg-gateway
#3
Tinyi Chu, Zhong Wang, Shao-Pei Chou, Charles G Danko
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...
December 27, 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30556956/using-omicsnet-for-network-integration-and-3d-visualization
#4
Guangyan Zhou, Jianguo Xia
OmicsNet is a novel web-based tool for creating and visualizing complex biological networks in 3D space. By coupling a comprehensive knowledgebase with the powerful WebGL technology, OmicsNet allows researchers to intuitively explore molecular interactions and regulatory relationships among genes, transcription factors, microRNAs, and metabolites. OmicsNet fills an important gap by facilitating multi-omics integration and systems biology. 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...
December 17, 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30489695/identification-of-key-residues-in-proteins-through-centrality-analysis-and-flexibility-prediction-with-rinspector
#5
Guillaume Brysbaert, Théo Mauri, Jérôme de Ruyck, Marc F Lensink
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 predicting backbone flexibility and needs only the primary sequence...
November 29, 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30485709/using-the-sorfs-org-database
#6
Volodimir Olexiouk, Gerben Menschaert
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 million sORFs across 78 datasets from six species...
November 28, 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30466165/predicting-genes-in-single-genomes-with-augustus
#7
Katharina J Hoff, Mario Stanke
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...
November 22, 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30422396/pre-processing-maldi-tof-mass-spectra-by-using-geena-2
#8
P Romano, A Profumo, A Facchiano
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...
December 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30422394/good-citizenship-made-easy-a-step-by-step-guide-to-submitting-rna-seq-data-to-ncbi
#9
Wiebke Feindt, Sara J Oppenheim, Robert DeSalle, Shaadi Mehr
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 deposition...
December 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30408350/investigation-of-rna-rna-interactions-using-the-rise-database
#10
Yanyan Ju, Jing Gong, Yucheng T Yang, Qiangfeng Cliff Zhang
RNA-RNA interactions (RRIs) are essential to understanding the regulatory mechanisms of RNAs. Mapping RRIs in vivo in a transcriptome-wide manner remained challenging until the recent development of several sequencing-based technologies. However, RRIs generated from large-scale studies had not been systematically collected and analyzed before. 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...
November 8, 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30332532/using-geneid-to-identify-genes
#11
Tyler Alioto, Enrique Blanco, Genís Parra, Roderic Guigó
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...
October 17, 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30168910/installing-maintaining-and-using-a-local-copy-of-blast-for-compute-cluster-or-workstation-use
#12
Istvan Ladunga
The Basic Local Alignment Search Tool (BLAST) is the first resource to computationally characterize a novel amino acid or nucleic acid sequence. BLAST plays important roles in genomics, transcriptomics, and protein science. For numerous academic and commercial researchers, neither BLAST Web servers nor cloud resources satisfy the requirements of high-throughput comparative genomic pipelines or company policies. For such users, this unit describes how to install BLAST locally, either on a standalone workstation, or preferably on a compute cluster...
September 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30168906/analysis-and-visualization-of-dynamic-networks-using-the-dynet-app-for-cytoscape
#13
John Salamon, Ivan H Goenawan, David J Lynn
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 the visualization and analysis of dynamic molecular interaction networks...
September 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30168903/improved-rna-seq-workflows-using-cyverse-cyberinfrastructure
#14
Kapeel M Chougule, Liya Wang, Joshua C Stein, Xiaofei Wang, Upendra Kumar Devisetty, Robert R Klein, Doreen Ware
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 use...
September 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/29927080/spin-submitting-sequences-determined-at-protein-level-to-uniprot
#15
Klemens Pichler, Kate Warner, Michele Magrane
Public availability of biological sequences is essential for their widespread access and use by the research community. The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and functional data. While most protein sequences entering UniProt are imported from other source databases containing nucleotide or 3-D structure data, protein sequences determined at the protein level can be submitted directly to UniProt. To this end, UniProt provides a Web interface called SPIN. This service enables researchers to make their de novo-sequenced proteins available to the scientific community and acquire UniProt accession numbers for use in publications...
June 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/29927076/the-gwips-viz-browser
#16
Stephen J Kiniry, Audrey M Michel, Pavel V Baranov
GWIPS-viz is a publicly available browser that provides Genome Wide Information on Protein Synthesis through the visualization of ribosome profiling data. Ribosome profiling (Ribo-seq) is a high-throughput technique which isolates fragments of messenger RNA that are protected by the ribosome. The alignment of the ribosome-protected fragments or footprint sequences to the corresponding reference genome and their visualization using GWIPS-viz allows for unique insights into the genome loci that are expressed as potentially translated RNA...
June 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/29927072/non-coding-rna-analysis-using-the-rfam-database
#17
Ioanna Kalvari, Eric P Nawrocki, Joanna Argasinska, Natalia Quinones-Olvera, Robert D Finn, Alex Bateman, Anton I Petrov
Rfam is a database of non-coding RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. Using a combination of manual and literature-based curation and a custom software pipeline, Rfam converts descriptions of RNA families found in the scientific literature into computational models that can be used to annotate RNAs belonging to those families in any DNA or RNA sequence. Valuable research outputs that are often locked up in figures and supplementary information files are encapsulated in Rfam entries and made accessible through the Rfam Web site...
June 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/29927069/using-lichee-and-bamse-for-reconstructing-cancer-phylogenetic-trees
#18
Camir Ricketts, Victoria Popic, Hosein Toosi, Iman Hajirasouliha
The reconstruction of cancer phylogeny trees and quantifying the evolution of the disease is a challenging task. LICHeE and BAMSE are two computational tools designed and implemented recently for this purpose. They both utilize estimated variant allele fraction of somatic mutations across multiple samples to infer the most likely cancer phylogenies. This unit provides extensive guidelines for installing and running both LICHeE and BAMSE. © 2018 by John Wiley & Sons, Inc.
June 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30040202/leveraging-experimental-details-for-an-improved-understanding-of-host-pathogen-interactome
#19
Mais Ammari, Fiona McCarthy, Bindu Nanduri
An increasing proportion of curated host-pathogen interaction (HPI) information is becoming available in interaction databases. These data represent detailed, experimentally-verified, molecular interaction data, which may be used to better understand infectious diseases. By their very nature, HPIs are context dependent, where the outcome of two proteins as interacting or not depends on the precise biological conditions studied and approaches used for identifying these interactions. The associated biology and the technical details of the experiments identifying interacting protein molecules are increasing being curated using defined curation standards but are overlooked in current HPI network modeling...
March 2018: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30040201/accessing-expert-curated-pharmacological-data-in-the-iuphar-bps-guide-to-pharmacology
#20
Joanna L Sharman, Simon D Harding, Christopher Southan, Elena Faccenda, Adam J Pawson, Jamie A Davies
The IUPHAR/BPS Guide to PHARMACOLOGY is an expert-curated, open-access database of information on drug targets and the substances that act on them. This unit describes the procedures for searching and downloading ligand-target binding data and for finding detailed annotations and the most relevant literature. The database includes concise overviews of the properties of 1,700 data-supported human drug targets and related proteins, divided into families, and 9,000 small molecule and peptide experimental ligands and approved drugs that bind to those targets...
March 2018: Current Protocols in Bioinformatics
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