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

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ISSN 1934-340X

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  • [Show abstract] [Hide abstract]
    ABSTRACT: The CATH database is a classification of protein structures found in the Protein Data Bank (PDB). Protein structures are chopped into individual units of structural domains, and these domains are grouped together into superfamilies if there is sufficient evidence that they have diverged from a common ancestor during the process of evolution. A sister resource, Gene3D, extends this information by scanning sequence profiles of these CATH domain superfamilies against many millions of known proteins to identify related sequences. Thus the combined CATH-Gene3D resource provides confident predictions of the likely structural fold, domain organisation, and evolutionary relatives of these proteins. In addition, this resource incorporates annotations from a large number of external databases such as known enzyme active sites, GO molecular functions, physical interactions, and mutations. This unit details how to access and understand the information contained within the CATH-Gene3D Web pages, the downloadable data files, and the remotely accessible Web services. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.
    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 06/2015; 50:1.28.1-1.28.21. DOI:10.1002/0471250953.bi0128s50
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    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.] 03/2015; 49:1.26.1-1.26.21. DOI:10.1002/0471250953.bi0126s49
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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.] 03/2015; 49:8.21.1-8.21.19. DOI:10.1002/0471250953.bi0821s49
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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: The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt Web site receives ∼400,000 unique visitors per month and is the primary means to access UniProt. It provides ten searchable datasets and three main tools. The key UniProt datasets are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), the UniProt Archive (UniParc), and protein sets for completely sequenced genomes (Proteomes). Other supporting datasets include information about proteins that is present in UniProtKB protein entries such as literature citations, taxonomy, and subcellular locations, among others. This paper focuses on how to use UniProt datasets. The basic protocol describes navigation and searching mechanisms for the UniProt datasets, while two alternative protocols build on the basic protocol to describe advanced search and query building. © 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; 50:1.27.1-1.27.10. DOI:10.1002/0471250953.bi0127s50
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    ABSTRACT: The Reactome project builds, maintains, and publishes a knowledgebase of biological pathways. The information in the knowledgebase is gathered from the experts in the field, peer reviewed and edited by Reactome editorial staff, and then published to the Reactome Web site, http://www.reactome.org. The Reactome software is open source and builds on top of other open-source or freely available software. Reactome data and code can be freely downloaded in its entirety and the Web site installed locally. This allows for more flexible interrogation of the data and also makes it possible to add one's own information to the knowledgebase. © 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; 50:9.10.1-9.10.10. DOI:10.1002/0471250953.bi0910s50
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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: 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.] 12/2014; 48:1.25.1-1.25.33. DOI:10.1002/0471250953.bi0125s48
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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.] 09/2014; 47:5.6.1-5.6.32. DOI:10.1002/0471250953.bi0506s47
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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.] 06/2014; 46:13.26.1-13.26.14. DOI:10.1002/0471250953.bi1326s46
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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: An overview of the many file formats commonly used in bioinformatics and genome sequence analysis is presented, including various data file formats, alignment file formats, and annotation file formats. Example workflows illustrate how some of the different file types are typically used. Curr. Protoc. Bioinform. 45:A.1B.1-A.1B.18. © 2014 by John Wiley & Sons, Inc.Keywords:file formats;bioinformatics;genomics
    Current Protocols in Bioinformatics, 03/2014: pages A.1B.1-A.1B.18; , ISBN: 9780471250951
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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: 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: 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: The European Bioinformatics Institute (EMBL-EBI) provides access to a wide range of databases and analysis tools that are of key importance in bioinformatics. As well as providing Web interfaces to these resources, Web Services are available using SOAP and REST protocols that enable programmatic access to our resources and allow their integration into other applications and analytical workflows. This unit describes the various options available to a typical researcher or bioinformatician who wishes to use our resources via Web interface or programmatically via a range of programming languages. © 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; 48:3.12.1-3.12.50. DOI:10.1002/0471250953.bi0312s48