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Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization.
Authors: Dhingra P, Fu Y, Gerstein M, Khurana E Abstract The identification of non-coding drivers remains a challenge and bottleneck for the use of whole-genome sequencing in the clinic. FunSeq2 is a computational tool for annotation and prioritization of somatic mutations in coding and non-coding regions. It integrates a data context made from large-scale genomic datasets and uses a high-throughput variant prioritization pipeline. This unit provides guidelines for installing and running FunSeq2 to (a) annotate and prioritize variants, (b) incorporate user-defined annotations, and (c) detect differential g...
Source: Current Protocols in Bioinformatics - May 4, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Phylogenetic Inference Using RevBayes.
Authors: Höhna S, Landis MJ, Heath TA Abstract Bayesian phylogenetic inference aims to estimate the evolutionary relationships among different lineages (species, populations, gene families, viral strains, etc.) in a model-based statistical framework that uses the likelihood function for parameter estimates. In recent years, evolutionary models for Bayesian analysis have grown in number and complexity. RevBayes uses a probabilistic-graphical model framework and an interactive scripting language for model specification to accommodate and exploit model diversity and complexity within a single software packag...
Source: Current Protocols in Bioinformatics - May 4, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using 3dRNA for RNA 3-D Structure Prediction and Evaluation.
Authors: Wang J, Xiao Y Abstract This unit describes how to use 3dRNA to predict RNA 3-D structures from their sequences and secondary (2-D) structures, and how to use 3dRNAscore to evaluate the predicted structures. The predicted RNA 3-D structures can be used to predict or understand their functions and can also be used to find the interactions between the RNA and other molecules. © 2017 by John Wiley & Sons, Inc. PMID: 28463400 [PubMed - in process] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - May 4, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data.
We describe both a simple one-shot run of cgpCaVEManWrapper and a more in-depth implementation suited to large-scale compute farms. © 2016 by John Wiley & Sons, Inc. PMID: 27930805 [PubMed - in process] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - December 10, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

The Search Engine for Multi-Proteoform Complexes: An Online Tool for the Identification and Stoichiometry Determination of Protein Complexes.
Authors: Skinner OS, Schachner LF, Kelleher NL Abstract Recent advances in top-down mass spectrometry using native electrospray now enable the analysis of intact protein complexes with relatively small sample amounts in an untargeted mode. Here, we describe how to characterize both homo- and heteropolymeric complexes with high molecular specificity using input data produced by tandem mass spectrometry of whole protein assemblies. The tool described is a "search engine for multi-proteoform complexes," (SEMPC) and is available for free online. The output is a list of candidate multi-proteoform complexes and ...
Source: Current Protocols in Bioinformatics - December 10, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Exploring FlyBase Data Using QuickSearch.
Authors: Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J, FlyBase Consortium Abstract FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data...
Source: Current Protocols in Bioinformatics - December 10, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype.
Authors: Shaw DR Abstract The Mouse Genome Informatics (MGI) resource provides the research community with access to information on the genetics, genomics, and biology of the laboratory mouse. Core data in MGI include gene characterization and function, phenotype and disease model descriptions, DNA and protein sequence data, gene expression data, vertebrate homologies, SNPs, mapping data, and links to other bioinformatics databases. Semantic integration is supported through the use of standardized nomenclature, and through the use of controlled vocabularies such as the mouse Anatomical Dictionary, the Mamm...
Source: Current Protocols in Bioinformatics - December 10, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data.
Authors: Raine KM, Van Loo P, Wedge DC, Jones D, Menzies A, Butler AP, Teague JW, Tarpey P, Nik-Zainal S, Campbell PJ Abstract We have developed ascatNgs to aid researchers in carrying out Allele-Specific Copy number Analysis of Tumours (ASCAT). ASCAT is capable of detecting DNA copy number changes affecting a tumor genome when comparing to a matched normal sample. Additionally, the algorithm estimates the amount of tumor DNA in the sample, known as Aberrant Cell Fraction (ACF). ASCAT itself is an R-package which requires the generation of many file types. Here, we present a suite of tools to help handle t...
Source: Current Protocols in Bioinformatics - December 10, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using the Tools and Resources of the RCSB Protein Data Bank.
Authors: Costanzo LD, Ghosh S, Zardecki C, Burley SK Abstract The Protein Data Bank (PDB) archive is the worldwide repository of experimentally determined three-dimensional structures of large biological molecules found in all three kingdoms of life. Atomic-level structures of these proteins, nucleic acids, and complex assemblies thereof are central to research and education in molecular, cellular, and organismal biology, biochemistry, biophysics, materials science, bioengineering, ecology, and medicine. Several types of information are associated with each PDB archival entry, including atomic coordinates,...
Source: Current Protocols in Bioinformatics - September 10, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

DIANA-TarBase and DIANA Suite Tools: Studying Experimentally Supported microRNA Targets.
Authors: Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG Abstract microRNAs (miRNAs) are short non-coding RNAs (∼22 nts) present in animals, plants, and viruses. They are considered central post-transcriptional regulators of gene expression and are key components in a great number of physiological and pathological conditions. The accurate characterization of their targets is considered essential to a series of applications and basic or applied research settings. DIANA-TarBase (http://www.microrna.gr/tarbase) was initially launched in 2006. It is a reference repository indexing experimentally derived miR...
Source: Current Protocols in Bioinformatics - September 10, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Obtaining miRNA-Target Interaction Information from miRWalk2.0.
This article describes a schematic workflow on how to obtain miRNA-target interactions from miRWalk2.0. © 2016 by John Wiley & Sons, Inc. PMID: 27603021 [PubMed - in process] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - September 10, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Tempest: Accelerated MS/MS Database Search Software for Heterogeneous Computing Platforms.
Authors: Adamo ME, Gerber SA Abstract MS/MS database search algorithms derive a set of candidate peptide sequences from in silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU (central processing unit) generates peptide candidates that are asynchronously sent to a discrete GPU (graphics processing unit) to be scored against experimental spectra in parallel. The current version of Tempest expands this model, ...
Source: Current Protocols in Bioinformatics - September 10, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis.
Authors: Xia J, Wishart DS Abstract MetaboAnalyst (http://www.metaboanalyst.ca) is a comprehensive Web application for metabolomic data analysis and interpretation. MetaboAnalyst handles most of the common metabolomic data types from most kinds of metabolomics platforms (MS and NMR) for most kinds of metabolomics experiments (targeted, untargeted, quantitative). In addition to providing a variety of data processing and normalization procedures, MetaboAnalyst also supports a number of data analysis and data visualization tasks using a range of univariate, multivariate methods such as PCA (principal componen...
Source: Current Protocols in Bioinformatics - September 10, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.
Authors: Stelzer G, Rosen N, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Stein TI, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary D, Warshawsky D, Guan-Golan Y, Kohn A, Rappaport N, Safran M, Lancet D Abstract GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the ...
Source: Current Protocols in Bioinformatics - June 21, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.
Authors: Barquist L, Burge SW, Gardner PP Abstract Emerging high-throughput technologies have led to a deluge of putative non-coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology detection is critical to making maximal use of functional information gathered about ncRNAs: identifying homologous sequence allows us to transfer information gathered in one organism to another quickly and with a high degree of confidence. ncRNA presents a challenge for homology detection, as the primary sequence is often ...
Source: Current Protocols in Bioinformatics - June 21, 2016 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research