Current Protocols in Bioinformatics 
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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.Installing, Maintaining, and Using a Local Copy of BLAST for Compute Cluster or Workstation Use.
Authors: Ladunga I
Abstract
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. We provide practical guidance fo...
Source: Current Protocols in Bioinformatics - September 2, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Exploring the Genetic Landscape of Metabolic Phenotypes with MetaboSignal.
Authors: Rodriguez-Martinez A, Ayala R, Posma JM, Dumas ME
Abstract
MetaboSignal is an R/Bioconductor package designed to explore the relationships between genes and metabolites, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) as its primary database. It is a network-based approach that allows overlaying metabolic and signaling pathways and exploring the topological relationship between genes (signaling or metabolic genes) and metabolites. MetaboSignal is ideally suited to identify candidate genes in metabolome genome-wide association studies (mGWAS), particularly in the case of trans-acting assoc...
Source: Current Protocols in Bioinformatics - July 25, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Network-Based Approaches for Pathway Level Analysis.
Authors: Nguyen T, Mitrea C, Draghici S
Abstract
Identification of impacted pathways is an important problem because it allows us to gain insights into the underlying biology beyond the detection of differentially expressed genes. In the past decade, a plethora of methods have been developed for this purpose. The last generation of pathway analysis methods are designed to take into account various aspects of pathway topology in order to increase the accuracy of the findings. Here, we cover 34 such topology-based pathway analysis methods published in the past 13 years. We compare these methods on categories...
Source: Current Protocols in Bioinformatics - July 25, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.
Authors: Salgado H, Martínez-Flores I, Bustamante VH, Alquicira-Hernández K, García-Sotelo JS, García-Alonso D, Collado-Vides J
Abstract
In RegulonDB, for over 25 years, we have been gathering knowledge by manual curation from original scientific literature on the regulation of transcription initiation and genome organization in transcription units of the Escherichia coli K-12 genome. This unit describes six basic protocols that can serve as a guiding introduction to the main content of the current version (v9.4) of this electronic resource. These protocols include general navigation as well as searchi...
Source: Current Protocols in Bioinformatics - July 25, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Exploring Biological Networks in 3D, Stereoscopic 3D, and Immersive 3D with iCAVE.
Authors: Kalayci S, Gümüş ZH
Abstract
Biological networks are becoming increasingly large and complex, pushing the limits of existing 2D tools. iCAVE is an open-source software tool for interactive visual explorations of large and complex networks in 3D, stereoscopic 3D, or immersive 3D. It introduces new 3D network layout algorithms and 3D extensions of popular 2D network layout, clustering, and edge bundling algorithms to assist researchers in understanding the underlying patterns in large, multi-layered, clustered, or complex networks. This protocol aims to guide new users on the basic functions of i...
Source: Current Protocols in Bioinformatics - July 25, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Searching ECOD for Homologous Domains by Sequence and Structure.
Authors: Schaeffer RD, Liao Y, Grishin NV
Abstract
ECOD is a database of evolutionary domains from structures deposited in the PDB. Domains in ECOD are classified by a mixed manual/automatic method wherein the bulk of newly deposited structures are classified automatically by protein-protein BLAST. Those structures that cannot be classified automatically are referred to manual curators who use a combination of alignment results, functional analysis, and close reading of the literature to generate novel assignments. ECOD differs from other structural domain resources in that it is continually updated, class...
Source: Current Protocols in Bioinformatics - July 25, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Accessing Expert-Curated Pharmacological Data in the IUPHAR/BPS Guide to PHARMACOLOGY.
Authors: Sharman JL, Harding SD, Southan C, Faccenda E, Pawson AJ, Davies JA, NC-IUPHAR
Abstract
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 a...
Source: Current Protocols in Bioinformatics - July 25, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Leveraging Experimental Details for an Improved Understanding of Host-Pathogen Interactome.
We describe the use of HPI data for network modeling, aspects of curation that can help researchers to more accurately model specific infection conditions, and provide examples to illustrate these principles. © 2018 by John Wiley & Sons, Inc.
PMID: 30040202 [PubMed - in process] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - July 25, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
EMDB Web Resources.
Authors: Abbott S, Iudin A, Korir PK, Somasundharam S, Patwardhan A
Abstract
The Electron Microscopy Data Bank (EMDB; http://emdb-empiar.org) is a global openly-accessible archive of biomolecular and cellular 3D reconstructions derived from electron microscopy (EM) data. EMBL-EBI develops web-based resources to facilitate the reuse of EMDB data. Here we provide protocols for how these resources can be used for searching EMDB, visualising EMDB structures, statistically analysing EMDB content and checking the validity of EMDB structures. Protocols for searching include quick link categories from the main pag...
Source: Current Protocols in Bioinformatics - July 18, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees.
Authors: Ricketts C, Popic V, Toosi H, Hajirasouliha I
Abstract
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.
PMID: 29927069 [PubMed - as supplied by publisher] (Source: ...
Source: Current Protocols in Bioinformatics - June 22, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Non-Coding RNA Analysis Using the Rfam Database.
This article gives an overview of how to search and navigate the Rfam Web site, and how to annotate sequences with RNA families. The Rfam database is freely available at http://rfam.org. © 2018 by John Wiley & Sons, Inc.
PMID: 29927072 [PubMed - as supplied by publisher] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - June 22, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
The GWIPS-viz Browser.
Authors: Kiniry SJ, Michel AM, Baranov PV
Abstract
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. The GWIPS-viz brows...
Source: Current Protocols in Bioinformatics - June 22, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
SPIN: Submitting Sequences Determined at Protein Level to UniProt.
Authors: Pichler K, Warner K, Magrane M, UniProt Consortium
Abstract
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 t...
Source: Current Protocols in Bioinformatics - June 22, 2018 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Prediction of Protein-Protein Interactions.
Authors: Kotlyar M, Rossos AEM, Jurisica I
Abstract
The authors provide an overview of physical protein-protein interaction prediction, covering the main strategies for predicting interactions, approaches for assessing predictions, and online resources for accessing predictions. This unit focuses on the main advancements in each of these areas over the last decade. The methods and resources that are presented here are not an exhaustive set, but characterize the current state of the field-highlighting key challenges and achievements. © 2017 by John Wiley & Sons, Inc.
PMID: 29220074 [PubMed - in...
Source: Current Protocols in Bioinformatics - December 10, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER.
This article describes how to use 3D-SURFER and EM-SURFER to carry out protein surface shape similarity searches, local geometric feature analysis, and interpretation of the search results. © 2017 by John Wiley & Sons, Inc.
PMID: 29220075 [PubMed - in process] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - December 10, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research
