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Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies (2013)

Schatz, M. C., Phillippy, A. M., Sommer, D. D., Delcher, A. L., Puiu, D., Narzisi, G., Salzberg, S. L., Pop, M.

Oxford University Press

In: Briefings in Bioinformatics

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Publikationsdatum: 2013-03-21

Beschreibung: Since its launch in 2004, the open-source AMOS project has released several innovative DNA sequence analysis applications including: Hawkeye, a visual analytics tool for inspecting the structure of genome assemblies; the Assembly Forensics and FRCurve pipelines for systematically evaluating the quality of a genome assembly; and AMOScmp, the first comparative genome assembler. These applications have been used to assemble and analyze dozens of genomes ranging in complexity from simple microbial species through mammalian genomes. Recent efforts have been focused on enhancing support for new data characteristics brought on by second- and now third-generation sequencing. This review describes the major components of AMOS in light of these challenges, with an emphasis on methods for assessing assembly quality and the visual analytics capabilities of Hawkeye. These interactive graphical aspects are essential for navigating and understanding the complexities of a genome assembly, from the overall genome structure down to individual bases. Hawkeye and AMOS are available open source at http://amos.sourceforge.net .

Print ISSN: 1467-5463

Digitale ISSN: 1477-4054

Thema: Biologie , Informatik

Publiziert von Oxford University Press

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The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability (2013)

Li, J.-W., Bolser, D., Manske, M., Giorgi, F. M., Vyahhi, N., Usadel, B., Clavijo, B. J., Chan, T.-F., Wong, N., Zerbino, D., Schneider, M. V.

Oxford University Press

In: Briefings in Bioinformatics

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Publikationsdatum: 2013-09-13

Beschreibung: Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.

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Thema: Biologie , Informatik

Publiziert von Oxford University Press

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Using Tablet for visual exploration of second-generation sequencing data (2013)

Milne, I., Stephen, G., Bayer, M., Cock, P. J. A., Pritchard, L., Cardle, L., Shaw, P. D., Marshall, D.

Oxford University Press

In: Briefings in Bioinformatics

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Publikationsdatum: 2013-03-21

Beschreibung: The advent of second-generation sequencing (2GS) has provided a range of significant new challenges for the visualization of sequence assemblies. These include the large volume of data being generated, short-read lengths and different data types and data formats associated with the diversity of new sequencing technologies. This article illustrates how Tablet—a high-performance graphical viewer for visualization of 2GS assemblies and read mappings—plays an important role in the analysis of these data. We present Tablet, and through a selection of use cases, demonstrate its value in quality assurance and scientific discovery, through features such as whole-reference coverage overviews, variant highlighting, paired-end read mark-up, GFF3-based feature tracks and protein translations. We discuss the computing and visualization techniques utilized to provide a rich and responsive graphical environment that enables users to view a range of file formats with ease. Tablet installers can be freely downloaded from http://bioinf.hutton.ac.uk/tablet in 32 or 64-bit versions for Windows, OS X, Linux or Solaris. For further details on the Tablet, contact tablet@hutton.ac.uk.

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Thema: Biologie , Informatik

Publiziert von Oxford University Press

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Obituary: In memory of Jack Leunissen (2013)

Luo, J., Nijveen, H., Attwood, T., Judge, D., Pongor, S., Landsman, D., Bishop, M.

Oxford University Press

In: Briefings in Bioinformatics

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Publikationsdatum: 2013-05-22

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Thema: Biologie , Informatik

Publiziert von Oxford University Press

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State-of-the-art technology in modern computer-aided drug design (2013)

Dalkas, G. A., Vlachakis, D., Tsagkrasoulis, D., Kastania, A., Kossida, S.

Oxford University Press

In: Briefings in Bioinformatics

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Publikationsdatum: 2013-11-10

Beschreibung: The quest for small drug-like compounds that selectively inhibit the function of biological targets has always been a major focus in the pharmaceutical industry and in academia as well. High-throughput screening of compound libraries requires time, cost and resources. Therefore, the use of alternative methods is necessary for facilitating lead discovery. Computational techniques that dock small molecules into macromolecular targets and predict the affinity and activity of the small molecule are widely used in drug design and discovery, and have become an integral part of the industrial and academic research. In this review, we present an overview of some state-of-the-art technologies in modern drug design that have been developed for expediting the search for novel drug candidates.

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Thema: Biologie , Informatik

Publiziert von Oxford University Press

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A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis (2013)

Dillies, M.-A., Rau, A., Aubert, J., Hennequet-Antier, C., Jeanmougin, M., Servant, N., Keime, C., Marot, G., Castel, D., Estelle, J., Guernec, G., Jagla, B., Jouneau, L., Laloe, D., Le Gall, C., Schaeffer, B., Le Crom, S., Guedj, M., Jaffrezic, F., on behalf of The French Stat; Omique Consortium

Oxford University Press

In: Briefings in Bioinformatics

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Publikationsdatum: 2013-11-10

Beschreibung: During the last 3 years, a number of approaches for the normalization of RNA sequencing data have emerged in the literature, differing both in the type of bias adjustment and in the statistical strategy adopted. However, as data continue to accumulate, there has been no clear consensus on the appropriate normalization method to be used or the impact of a chosen method on the downstream analysis. In this work, we focus on a comprehensive comparison of seven recently proposed normalization methods for the differential analysis of RNA-seq data, with an emphasis on the use of varied real and simulated datasets involving different species and experimental designs to represent data characteristics commonly observed in practice. Based on this comparison study, we propose practical recommendations on the appropriate normalization method to be used and its impact on the differential analysis of RNA-seq data.

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Thema: Biologie , Informatik

Publiziert von Oxford University Press

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7

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Batch effect removal methods for microarray gene expression data integration: a survey (2013)

Lazar, C., Meganck, S., Taminau, J., Steenhoff, D., Coletta, A., Molter, C., Weiss-Solis, D. Y., Duque, R., Bersini, H., Nowe, A.

Oxford University Press

In: Briefings in Bioinformatics

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Publikationsdatum: 2013-07-18

Beschreibung: Genomic data integration is a key goal to be achieved towards large-scale genomic data analysis. This process is very challenging due to the diverse sources of information resulting from genomics experiments. In this work, we review methods designed to combine genomic data recorded from microarray gene expression (MAGE) experiments. It has been acknowledged that the main source of variation between different MAGE datasets is due to the so-called ‘batch effects’. The methods reviewed here perform data integration by removing (or more precisely attempting to remove) the unwanted variation associated with batch effects. They are presented in a unified framework together with a wide range of evaluation tools, which are mandatory in assessing the efficiency and the quality of the data integration process. We provide a systematic description of the MAGE data integration methodology together with some basic recommendation to help the users in choosing the appropriate tools to integrate MAGE data for large-scale analysis; and also how to evaluate them from different perspectives in order to quantify their efficiency. All genomic data used in this study for illustration purposes were retrieved from InSilicoDB http://insilico.ulb.ac.be .

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Thema: Biologie , Informatik

Publiziert von Oxford University Press

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Obituary: In memory of Jack Leunissen (2013)

Luo, J. ; Nijveen, H. ; Attwood, T. ; [weitere]

Oxford University Press

In: Briefings in Bioinformatics. 2013; 14(3): 261-262. Published 2013 May 01. doi: 10.1093/bib/bbt036.

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Publikationsdatum: 2013-05-01

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Thema: Biologie , Informatik

Publiziert von Oxford University Press

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The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability (2013)

Li, J.-W. ; Bolser, D. ; Manske, M. ; [weitere]

Oxford University Press

In: Briefings in Bioinformatics. 2013; 14(5): 548-555. Published 2013 Jun 21. doi: 10.1093/bib/bbt045.

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Publikationsdatum: 2013-06-21

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Thema: Biologie , Informatik

Publiziert von Oxford University Press

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Navigating the changing learning landscape: perspective from bioinformatics.ca (2013)

Brazas, M. D., Ouellette, B. F. F.

Oxford University Press

In: Briefings in Bioinformatics

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Publikationsdatum: 2013-09-13

Beschreibung: With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs.

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Thema: Biologie , Informatik

Publiziert von Oxford University Press

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