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Bioinformatics

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  1. Content type: Technical Note

    Genome assembly is a fundamental problem with multiple applications. Current technological limitations do not allow assembling of entire genomes and many programs have been designed to produce longer and more ...

    Authors: Nilesh Khiste and Lucian Ilie

    Citation: BMC Research Notes 2015 8:709

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  2. Content type: Research article

    Under postharvest physiological deterioration cassava root tubers alter the expression of biosynthetic pathways of certain primary and secondary metabolites, as well as the activity of some scavenging enzymes....

    Authors: Virgílio Gavicho Uarrota and Marcelo Maraschin

    Citation: BMC Research Notes 2015 8:648

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  3. Content type: Technical Note

    One of the requirements for a successful scientific tool is its availability. Developing a functional web service, however, is usually considered a mundane and ungratifying task, and quite often neglected. Whe...

    Authors: Paweł Daniluk, Bartek Wilczyński and Bogdan Lesyng

    Citation: BMC Research Notes 2015 8:628

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  4. Content type: Short Report

    To demonstrate the bioinformatics capabilities of a low-cost computer, the Raspberry Pi, we present a comparison of the protein-coding gene content of two species in phylum Chlamydiae: Chlamydia trachomatis, a co...

    Authors: James F. Robson and Daniel Barker

    Citation: BMC Research Notes 2015 8:561

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  5. Content type: Technical Note

    With the advent of high-throughput sequencing technologies large-scale identification of microsatellites became affordable and was especially directed to non-model species. By contrast, few efforts have been p...

    Authors: Concita Cantarella and Nunzio D’Agostino

    Citation: BMC Research Notes 2015 8:525

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  6. Content type: Research article

    Inflammatory disease processes involve complex and interrelated systems of mediators. Determining the causal relationships among these mediators becomes more complicated when two, concurrent inflammatory condi...

    Authors: Jean A. Nemzek, Andrew P. Hodges and Yongqun He

    Citation: BMC Research Notes 2015 8:516

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  7. Content type: Technical Note

    For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microb...

    Authors: Se-Ran Jun, Michael S. Robeson, Loren J. Hauser, Christopher W. Schadt and Andrey A. Gorin

    Citation: BMC Research Notes 2015 8:479

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  8. Content type: Research article

    Every next generation sequencing (NGS) platform relies on proprietary and open source computational tools to analyze sequencing data. NGS tools for Illumina platforms are well documented which is not the case ...

    Authors: Erinija Pranckevičiene, Tautvydas Rančelis, Aidas Pranculis and Vaidutis Kučinskas

    Citation: BMC Research Notes 2015 8:421

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  9. Content type: Technical Note

    Next-generation sequencing allows for determining the genetic composition of a mixed sample. For instance, when performing resistance testing for BCR-ABL1 it is necessary to identify clones and define compound mu...

    Authors: Norbert Niklas, Julia Hafenscher, Agnes Barna, Karin Wiesinger, Johannes Pröll, Stephan Dreiseitl, Sandra Preuner-Stix, Peter Valent, Thomas Lion and Christian Gabriel

    Citation: BMC Research Notes 2015 8:422

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  10. Content type: Technical Note

    Next generation sequencing (NGS) data treatment often requires mapping sequenced reads onto a reference genome for further analysis. Mapped data are commonly visualized using genome browsers. However, such sof...

    Authors: Marc Descrimes, Yousra Ben Zouari, Maxime Wery, Rachel Legendre, Daniel Gautheret and Antonin Morillon

    Citation: BMC Research Notes 2015 8:419

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  11. Content type: Research article

    Genotype imputation is an important procedure in current genomic analysis such as genome-wide association studies, meta-analyses and fine mapping. Although high quality tools are available that perform the ste...

    Authors: Alexandros Kanterakis, Patrick Deelen, Freerk van Dijk, Heorhiy Byelas, Martijn Dijkstra and Morris A Swertz

    Citation: BMC Research Notes 2015 8:359

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  12. Content type: Research article

    In recent years the emergence of multidrug resistant Klebsiella pneumoniae strains has been an increasingly common event. This opportunistic species is one of the five main bacterial pathogens that cause hospital...

    Authors: Martha Lorena Ostria-Hernández, Carlos Javier Sánchez-Vallejo, J Antonio Ibarra and Graciela Castro-Escarpulli

    Citation: BMC Research Notes 2015 8:332

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  13. Content type: Technical Note

    Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can ...

    Authors: Eric van der Helm, Henrik Marcus Geertz-Hansen, Hans Jasper Genee, Sailesh Malla and Morten Otto Alexander Sommer

    Citation: BMC Research Notes 2015 8:328

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  14. Content type: Research article

    Proteolytic enzymes are ubiquitous and active in a myriad of biochemical pathways. One type, the rhomboids are intramembrane serine proteases that release their products extracellularly. These proteases are pr...

    Authors: Peter A Novick, Naydu M Carmona and Monica Trujillo

    Citation: BMC Research Notes 2015 8:234

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