Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]

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ISSN 1934-340X

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: SCOP2 is a successor to the Structural Classification of Proteins (SCOP) database that organizes proteins of known structure according to their structural and evolutionary relationships. It was designed to provide a more advanced framework for the classification of proteins. The SCOP2 classification is described in terms of a directed acyclic graph in which each node defines a relationship of particular type that is represented by a region of protein structure and sequence. The SCOP2 data are accessible via SCOP2-Browser and SCOP2-Graph. This protocol unit describes different ways to explore and investigate the SCOP2 evolutionary and structural groupings. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2015; 49:1.26.1-1.26.21. DOI:10.1002/0471250953.bi0126s49
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    ABSTRACT: RNA editing is a post-transcriptional/co-transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions. It occurs in a variety of organisms and different cellular locations through evolutionally and biochemically unrelated proteins. RNA editing has a plethora of biological effects including the modulation of alternative splicing and fine-tuning of gene expression. RNA editing events by base substitutions can be detected on a genomic scale by NGS technologies through the REDItools package, an ad hoc suite of Python scripts to study RNA editing using RNA-Seq and DNA-Seq data or RNA-Seq data alone. REDItools implement effective filters to minimize biases due to sequencing errors, mapping errors, and SNPs. The package is freely available at Google Code repository (http://code.google.com/p/reditools/) and released under the MIT license. In the present unit we show three basic protocols corresponding to three main REDItools scripts. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2015; 49:12.12.1-12.12.15. DOI:10.1002/0471250953.bi1212s49
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    ABSTRACT: pLink is a search engine for high-throughput identification of cross-linked peptides from their tandem mass spectra, which is the data-analysis step in chemical cross-linking of proteins coupled with mass spectrometry analysis. pLink has accumulated more than 200 registered users from all over the world since its first release in 2012. After 2 years of continual development, a new version of pLink has been released, which is at least 40 times faster, more versatile, and more user-friendly. Also, the function of the new pLink has been expanded to identifying endogenous protein cross-linking sites such as disulfide bonds and SUMO (Small Ubiquitin-like MOdifier) modification sites. Integrated into the new version are two accessory tools: pLabel, to annotate spectra of cross-linked peptides for visual inspection and publication, and pConfig, to assist users in setting up search parameters. Here, we provide detailed guidance on running a database search for identification of protein cross-links using the 2014 version of pLink. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2015; 49:8.21.1-8.21.19. DOI:10.1002/0471250953.bi0821s49
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    ABSTRACT: The Reactome database of curated biological pathways provides a tool for visualizing user-supplied expression data as an overlay on pathway diagrams, thereby affording an effective means to examine expression of the constituents of the pathway and determine whether all that are necessary are present. Several experiments can be visualized in succession, to determine whether expression changes with experimental conditions, a useful feature for examining a time-course, dose-response, or disease progression. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2015; 49:8.20.1-9. DOI:10.1002/0471250953.bi0820s49
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    ABSTRACT: High-throughput Affinity Purification Mass Spectrometry (AP-MS) experiments can identify a large number of protein interactions, but only a fraction of these interactions are biologically relevant. Here, we describe a comprehensive computational strategy to process raw AP-MS data, perform quality controls, and prioritize biologically relevant bait-prey pairs in a set of replicated AP-MS experiments with Mass spectrometry interaction STatistics (MiST). The MiST score is a linear combination of prey quantity (abundance), abundance invariability across repeated experiments (reproducibility), and prey uniqueness relative to other baits (specificity). We describe how to run the full MiST analysis pipeline in an R environment and discuss a number of configurable options that allow the lay user to convert any large-scale AP-MS data into an interpretable, biologically relevant protein-protein interaction network. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2015; 49:8.19.1-8.19.16. DOI:10.1002/0471250953.bi0819s49
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    ABSTRACT: VisANT is a Web-based workbench for the integrative analysis of biological networks with unique features such as exploratory navigation of interaction network and multi-scale visualization and inference with integrated hierarchical knowledge. It provides functionalities for convenient construction, visualization, and analysis of molecular and higher order networks based on functional (e.g., expression profiles, phylogenetic profiles) and physical (e.g., yeast two-hybrid, chromatin-immunoprecipitation and drug target) relations from either the Predictome database or user-defined data sets. Analysis capabilities include network structure analysis, overrepresentation analysis, expression enrichment analysis etc. Additionally, network can be saved, accessed, and shared online. VisANT is able to develop and display meta-networks for meta-nodes that are structural complexes or pathways or any kind of subnetworks. Further, VisANT supports a growing number of standard exchange formats and database referencing standards, e.g., PSI-MI, KGML, BioPAX, SBML(in progress) Multiple species are supported to the extent that interactions or associations are available (i.e., public datasets or Predictome database).
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 03/2014; 8(88):8.8.1-8.8.39. DOI:10.1002/0471250953.bi0808s45
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    ABSTRACT: Detecting somatic single nucleotide variants (SNVs) is an essential component of cancer research with next generation sequencing data. This protocol describes how to run the SomaticSniper somatic SNV detector and then filter the output to eliminate most false positives. It also includes support protocols detailing the compilation of the software.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 03/2014; 15(155):15.5.1-15.5.8. DOI:10.1002/0471250953.bi1505s45
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    ABSTRACT: One of the greatest challenges facing modern molecular biology is understanding the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of sequence motifs involved in the regulation of gene expression at transcriptional and post-transcriptional levels. In particular, transcription is modulated by the interaction of transcription factors (TFs) with their corresponding binding sites. Weeder, Pscan, and PscanChIP are software tools freely available for noncommercial users as a stand-alone or Web-based applications for the automatic discovery of conserved motifs in a set of DNA sequences likely to be bound by the same TFs. Input for the tools can be promoter sequences from co-expressed or co-regulated genes (for which Weeder and Pscan are suitable), or regions identified through genome wide ChIP-seq or similar experiments (Weeder and PscanChIP). The motifs are either found by a de novo approach (Weeder) or by using descriptors of the binding specificity of TFs (Pscan and PscanChIP). Curr. Protoc. Bioinform. 47:2.11.1-2.11.31. © 2014 by John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2014; 47:2.11.1-2.11.31. DOI:10.1002/0471250953.bi0211s47
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    ABSTRACT: This unit describes how to use the genome annotation and curation tools MAKER and MAKER-P to annotate protein-coding and noncoding RNA genes in newly assembled genomes, update/combine legacy annotations in light of new evidence, add quality metrics to annotations from other pipelines, and map existing annotations to a new assembly. MAKER and MAKER-P can rapidly annotate genomes of any size, and scale to match available computational resources. © 2014 by John Wiley & Sons, Inc. Copyright © 2014 John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2014; 48:4.11.1-4.11.39. DOI:10.1002/0471250953.bi0411s48
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    ABSTRACT: Technological advances have enabled the use of DNA sequencing as a flexible tool to characterize genetic variation and to measure the activity of diverse cellular phenomena such as gene isoform expression and transcription factor binding. Extracting biological insight from the experiments enabled by these advances demands the analysis of large, multi-dimensional datasets. This unit describes the use of the BEDTools toolkit for the exploration of high-throughput genomics datasets. Several protocols are presented for common genomic analyses, demonstrating how simple BEDTools operations may be combined to create bespoke pipelines addressing complex questions. Curr. Protoc. Bioinform. 47:11.12.1-11.12.34. © 2014 by John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2014; 47:11.12.1-11.12.34. DOI:10.1002/0471250953.bi1112s47
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    ABSTRACT: Systems medicine provides insights into mechanisms of human diseases, and expedites the development of better diagnostics and drugs. To facilitate such strategies, we initiated MalaCards, a compendium of human diseases and their annotations, integrating and often remodeling information from 64 data sources. MalaCards employs, among others, the proven automatic data-mining strategies established in the construction of GeneCards, our widely used compendium of human genes. The development of MalaCards poses many algorithmic challenges, such as disease name unification, integrated classification, gene-disease association, and disease-targeted expression analysis. MalaCards displays a Web card for each of >19,000 human diseases, with 17 sections, including textual summaries, related diseases, related genes, genetic variations and tests, and relevant publications. Also included are a powerful search engine and a variety of categorized disease lists. This unit describes two basic protocols to search and browse MalaCards effectively. Curr. Protoc. Bioinform. 47:1.24.1-1.24.19. © 2014 by John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2014; 47:1.24.1-1.24.19. DOI:10.1002/0471250953.bi0124s47
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    ABSTRACT: Clustal Omega is a package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately. It is a complete upgrade and rewrite of earlier Clustal programs. This unit describes how to run Clustal Omega interactively from a command line, although it can also be run online from several sites. The unit describes a basic protocol for taking a set of unaligned sequences and producing a full alignment. There are also protocols for using an external HMM or iteration to help improve an alignment. © 2014 by John Wiley & Sons, Inc. Copyright © 2014 John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2014; 48:3.13.1-3.13.16. DOI:10.1002/0471250953.bi0313s48
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    ABSTRACT: Cross-linking combined with mass spectrometry for the study of proteins and protein complexes is greatly facilitated by the use of isotopically coded cleavable cross-linking reagents. The isotopic coding of the cross-linker enables confident detection of the cross-link signals, while cleavage of the cross-linker provides masses of the individual peptides composing the cross-link and, therefore, facilitates unambiguous assignment of the cross-links. Here, we describe the DXMSMS Match program, designed for automatic analysis of LC-MS/MS mass spectrometric data obtained with isotopically coded CID-cleavable cross-linkers. The program verifies the assignments of the cross-links by precursor mass and by inspection of the MS/MS spectra for the fragments and the cleavage products of the cross-linked peptides. The program produces nonprobabilistic scores for matching the spectra to the theoretical fragmentation of the cross-links and a visual interface for the validation of the mass spectral matches. © 2014 by John Wiley & Sons, Inc. Copyright © 2014 John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2014; 48:8.18.1-8.18.19. DOI:10.1002/0471250953.bi0818s48
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    ABSTRACT: MEROPS is a database of proteolytic enzymes as well as their inhibitors and substrates. Proteolytic enzymes and protein inhibitors are organized into protein domain families. In turn, families are organized into clans. Each peptidase, inhibitor, family, and clan has associated annotation, a multiple sequence alignment, a phylogenetic tree, literature references, and links to other databases. Interactions between proteolytic enzymes and inhibitors and between proteolytic enzymes and substrates are also presented. The entries in MEROPS are available via the World Wide Web. This unit contains detailed information on how to access and utilize the information present in the MEROPS database. Details on running MEROPS both remotely and locally are presented. © 2014 by John Wiley & Sons, Inc. Copyright © 2014 John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2014; 48:1.25.1-1.25.33. DOI:10.1002/0471250953.bi0125s48
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    ABSTRACT: PeptideAtlas, SRMAtlas, and PASSEL are Web-accessible resources to support discovery and targeted proteomics research. PeptideAtlas is a multi-species compendium of shotgun proteomic data provided by the scientific community; SRMAtlas is a resource of high-quality, complete proteome SRM assays generated in a consistent manner for the targeted identification and quantification of proteins; and PASSEL is a repository that compiles and represents selected reaction monitoring data, all in an easy-to-use interface. The databases are generated from native mass spectrometry data files that are analyzed in a standardized manner including statistical validation of the results. Each resource offers search functionalities and can be queried by user-defined constraints; the query results are provided in tables or are graphically displayed. PeptideAtlas, SRMAtlas, and PASSEL are publicly available freely via the Web site http://www.peptideatlas.org. In this protocol, we describe the use of these resources, we highlight how to submit, search, collate and download data. Curr. Protoc. Bioinform. 46:13.25.1-13.25.28. © 2014 by John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2014; 46:13.25.1-13.25.28. DOI:10.1002/0471250953.bi1325s46
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    ABSTRACT: The structures of many non-coding RNA (ncRNA) are conserved by evolution to a greater extent than their sequences. By predicting the conserved structure of two or more homologous sequences, the accuracy of secondary structure prediction can be improved as compared to structure prediction for a single sequence. This unit provides protocols for the use of four programs in the RNAstructure suite for prediction of conserved structures, Multilign, TurboFold, Dynalign, and PARTS. These programs can be run via Web servers, on the command line, or with graphical interfaces. Curr. Protoc. Bioinform. 46:12.4.1-12.4.22. © 2014 by John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2014; 46:12.4.1-12.4.22. DOI:10.1002/0471250953.bi1204s46
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    ABSTRACT: Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. Curr. Protoc. Bioinform. 46:13.26.1-13.26.14. © 2014 by John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2014; 46:13.26.1-13.26.14. DOI:10.1002/0471250953.bi1326s46
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    ABSTRACT: Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. Curr. Protoc. Bioinform. 47:5.6.1-5.6.32. © 2014 by John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 01/2014; 47:5.6.1-5.6.32. DOI:10.1002/0471250953.bi0506s47