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

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ISSN 1934-340X

Publications in this journal

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    ABSTRACT: Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates, providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, and signal visualization. In this unit, we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is open source software that can be run on Unix, Linux, or Mac OS X systems. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.
    No preview · Article · Sep 2015 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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    ABSTRACT: Transcription factors (TFs) recognize and bind to specific DNA sequences. The specificity of a TF is usually represented as a position weight matrix (PWM). Several databases of DNA motifs exist and are used in biological research to address important biological questions. This overview describes PWMs and some of the most commonly used motif databases, as well as a few of their common applications. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.
    No preview · Article · Sep 2015 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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    ABSTRACT: The characterization of new genomes based on their protein sets has been revolutionized by new sequencing technologies, but biologists seeking to exploit new sequence information are often frustrated by the challenges associated with accurately assigning biological functions to newly identified proteins. Here, we highlight some of the challenges in functional inference from sequence similarity. Investigators can improve the accuracy of function prediction by (1) being conservative about the evolutionary distance to a protein of known function; (2) considering the ambiguous meaning of "functional similarity," and (3) being aware of the limitations of annotations in functional databases. Protein function prediction does not offer "one-size-fits-all" solutions. Prediction strategies work better when the idiosyncrasies of function and functional annotation are better understood. © 2015 by John Wiley & Sons, Inc.
    No preview · Article · Sep 2015 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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    ABSTRACT: Cloud Computing refers to distributed computing platforms that use virtualization software to provide easy access to physical computing infrastructure and data storage, typically administered through a Web interface. Cloud-based computing provides access to powerful servers, with specific software and virtual hardware configurations, while eliminating the initial capital cost of expensive computers and reducing the ongoing operating costs of system administration, maintenance contracts, power consumption, and cooling. This eliminates a significant barrier to entry into bioinformatics and high-performance computing for many researchers. This is especially true of free or modestly priced cloud computing services. The iPlant Collaborative offers a free cloud computing service, Atmosphere, which allows users to easily create and use instances on virtual servers preconfigured for their analytical needs. Atmosphere is a self-service, on-demand platform for scientific computing. This unit demonstrates how to set up, access and use cloud computing in Atmosphere. Curr. Protoc. Bioinform. 43:9.15.1-9.15.20. © 2013 by John Wiley & Sons, Inc.
    No preview · Article · Aug 2015 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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    ABSTRACT: Modern Illumina-like high-throughput sequencing machines allow the cheap decoding of great amounts of DNA. The GEnomic Multi-tool (GEM) mapper is one of the fastest and most sensitive methods known to date to align such data to a known genomic reference. This unit explains how to use it effectively. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.
    No preview · Article · Jun 2015 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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    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.
    No preview · Article · Jun 2015 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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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.
    No preview · Article · Jun 2015 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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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.
    No preview · Article · Jun 2015 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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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.
    No preview · Article · Mar 2015 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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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.
    No preview · Article · Mar 2015 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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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.
    No preview · Article · Mar 2015 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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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.
    No preview · Article · Dec 2014 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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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.
    No preview · Article · Dec 2014 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
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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.
    No preview · Article · Dec 2014 · Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]