Bioinformatics

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  1. Research article

    A computational protocol to evaluate the effects of protein mutants in the kinase gatekeeper position on the binding of ATP substrate analogues

    The determination of specific kinase substrates in vivo is challenging due to the large number of protein kinases in cells, their substrate specificity overlap, and the lack of highly specific inhibitors. In t...

    Valentina Romano, Tjaart A. P. de Beer and Torsten Schwede

    BMC Research Notes 2017 10:104

    Published on: 20 February 2017

  2. Technical Note

    Differential correlation for sequencing data

    Several methods have been developed to identify differential correlation (DC) between pairs of molecular features from –omics studies. Most DC methods have only been tested with microarrays and other platforms...

    Charlotte Siska and Katerina Kechris

    BMC Research Notes 2017 10:54

    Published on: 19 January 2017

  3. Research article

    An evaluation of the evolution of the gene structure of dystroglycan

    Dystroglycan (DG) is an adhesion receptor complex composed of two non-covalently associated subunits, transcribed from a single gene. The extracellular α-DG is highly and heterogeneously glycosylated and binds...

    Andrea Brancaccio and Josephine C. Adams

    BMC Research Notes 2017 10:19

    Published on: 3 January 2017

  4. Research article

    Mycofier: a new machine learning-based classifier for fungal ITS sequences

    The taxonomic and phylogenetic classification based on sequence analysis of the ITS1 genomic region has become a crucial component of fungal ecology and diversity studies. Nowadays, there is no accurate alignm...

    Luisa Delgado-Serrano, Silvia Restrepo, Jose Ricardo Bustos, Maria Mercedes Zambrano and Juan Manuel Anzola

    BMC Research Notes 2016 9:402

    Published on: 11 August 2016

  5. Technical Note

    DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses

    DNA metabarcoding is an approach for identifying multiple taxa in an environmental sample using specific genetic loci and taxa-specific primers. When combined with high-throughput sequencing it enables the tax...

    Marie Lisandra Zepeda-Mendoza, Kristine Bohmann, Aldo Carmona Baez and M. Thomas P. Gilbert

    BMC Research Notes 2016 9:255

    Published on: 3 May 2016

  6. Technical Note

    CABRA: Cluster and Annotate Blast Results Algorithm

    Basic local alignment search tool (BLAST) searches are frequently used to look for homologous sequences and to annotate a query protein, but the increasing size of protein databases makes it difficult to revie...

    Pablo Mier and Miguel A. Andrade-Navarro

    BMC Research Notes 2016 9:253

    Published on: 30 April 2016

  7. Technical Note

    HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants

    Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits and diseases. However, most of them are located in the non-protein coding regions, and theref...

    Zheng Xu, Guosheng Zhang, Qing Duan, Shengjie Chai, Baqun Zhang, Cong Wu, Fulai Jin, Feng Yue, Yun Li and Ming Hu

    BMC Research Notes 2016 9:159

    Published on: 11 March 2016

  8. Technical Note

    blastjs: a BLAST+ wrapper for Node.js

    To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- a...

    Martin Page, Dan MacLean and Christian Schudoma

    BMC Research Notes 2016 9:130

    Published on: 27 February 2016

  9. Research article

    A web-oriented software for the optimization of pooled experiments in NGS for detection of rare mutations

    The cost per patient of next generation sequencing for detection of rare mutations may be significantly reduced using pooled experiments. Recently, some techniques have been proposed for the planning of pooled...

    Daniela Evangelista, Antonio Zuccaro, Algirdas Lančinskas, Julius Žilinskas and Mario R. Guarracino

    BMC Research Notes 2016 9:111

    Published on: 17 February 2016

  10. Technical Note

    SeqTools: visual tools for manual analysis of sequence alignments

    Manual annotation is essential to create high-quality reference alignments and annotation. Annotators need to be able to view sequence alignments in detail. The SeqTools package provides three tools for viewin...

    Gemma Barson and Ed Griffiths

    BMC Research Notes 2016 9:39

    Published on: 22 January 2016

  11. Research article

    A cancer cell-line titration series for evaluating somatic classification

    Accurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated w...

    Robert E. Denroche, Laura Mullen, Lee Timms, Timothy Beck, Christina K. Yung, Lincoln Stein, John D. McPherson and Andrew M. K. Brown

    BMC Research Notes 2015 8:823

    Published on: 26 December 2015

  12. Technical Note

    iTAP: integrated transcriptomics and phenotype database for stress response of Escherichia coli and Saccharomyces cerevisiae

    Organisms are subject to various stress conditions, which affect both the organism’s gene expression and phenotype. It is critical to understand microbial responses to stress conditions and uncover the underly...

    Niveda Sundararaman, Christine Ash, Weihua Guo, Rebecca Button, Jugroop Singh and Xueyang Feng

    BMC Research Notes 2015 8:771

    Published on: 12 December 2015

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