Sequence analysis (methods)

Section edited by Olivier Poch

This section incorporates all aspects of sequence analysis methodology, including but not limited to: sequence alignment algorithms, discrete algorithms, phylogeny algorithms, gene prediction and sequence clustering methods.

Previous Page Page 1 of 18 Next Page
  1. Software

    eccCL: parallelized GPU implementation of Ensemble Classifier Chains

    Multi-label classification has recently gained great attention in diverse fields of research, e.g., in biomedical application such as protein function prediction or drug resistance testing in HIV. In this cont...

    Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch and Dominik Heider

    BMC Bioinformatics 2017 18:371

    Published on: 17 August 2017

  2. Research Article

    Improving fold resistance prediction of HIV-1 against protease and reverse transcriptase inhibitors using artificial neural networks

    Drug resistance in HIV treatment is still a worldwide problem. Predicting resistance to antiretrovirals (ARVs) before starting any treatment is important. Prediction accuracy is essential, as low-accuracy pred...

    Olivier Sheik Amamuddy, Nigel T. Bishop and Özlem Tastan Bishop

    BMC Bioinformatics 2017 18:369

    Published on: 15 August 2017

  3. Research Article

    Local sequence and sequencing depth dependent accuracy of RNA-seq reads

    Many biases and spurious effects are inherent in RNA-seq technology, resulting in a non-uniform distribution of sequencing read counts for each base position in a gene. Therefore, a base-level strategy is requ...

    Guoshuai Cai, Shoudan Liang, Xiaofeng Zheng and Feifei Xiao

    BMC Bioinformatics 2017 18:364

    Published on: 9 August 2017

  4. Software

    Repliscan: a tool for classifying replication timing regions

    Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density...

    Gregory J. Zynda, Jawon Song, Lorenzo Concia, Emily E. Wear, Linda Hanley-Bowdoin, William F. Thompson and Matthew W. Vaughn

    BMC Bioinformatics 2017 18:362

    Published on: 7 August 2017

  5. Methodology Article

    Correcting nucleotide-specific biases in high-throughput sequencing data

    High-throughput sequence (HTS) data exhibit position-specific nucleotide biases that obscure the intended signal and reduce the effectiveness of these data for downstream analyses. These biases are particularl...

    Jeremy R. Wang, Bryan Quach and Terrence S. Furey

    BMC Bioinformatics 2017 18:357

    Published on: 1 August 2017

  6. Methodology Article

    Quantification of tumour evolution and heterogeneity via Bayesian epiallele detection

    Epigenetic heterogeneity within a tumour can play an important role in tumour evolution and the emergence of resistance to treatment. It is increasingly recognised that the study of DNA methylation (DNAm) patt...

    James E. Barrett, Andrew Feber, Javier Herrero, Miljana Tanic, Gareth A. Wilson, Charles Swanton and Stephan Beck

    BMC Bioinformatics 2017 18:354

    Published on: 25 July 2017

  7. Research article

    Identifying and mitigating batch effects in whole genome sequencing data

    Large sample sets of whole genome sequencing with deep coverage are being generated, however assembling datasets from different sources inevitably introduces batch effects. These batch effects are not well und...

    Jennifer A. Tom, Jens Reeder, William F. Forrest, Robert R. Graham, Julie Hunkapiller, Timothy W. Behrens and Tushar R. Bhangale

    BMC Bioinformatics 2017 18:351

    Published on: 24 July 2017

  8. Methodology Article

    SegCorr a statistical procedure for the detection of genomic regions of correlated expression

    Detecting local correlations in expression between neighboring genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been s...

    Eleni Ioanna Delatola, Emilie Lebarbier, Tristan Mary-Huard, François Radvanyi, Stéphane Robin and Jennifer Wong

    BMC Bioinformatics 2017 18:333

    Published on: 11 July 2017

  9. Software

    HLA-check: evaluating HLA data from SNP information

    The major histocompatibility complex (MHC) region of the human genome, and specifically the human leukocyte antigen (HLA) genes, play a major role in numerous human diseases. With the recent progress of sequen...

    Marc Jeanmougin, Josselin Noirel, Cédric Coulonges and Jean-François Zagury

    BMC Bioinformatics 2017 18:334

    Published on: 11 July 2017

  10. Methodology Article

    An improved filtering algorithm for big read datasets and its application to single-cell assembly

    For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This lea...

    Axel Wedemeyer, Lasse Kliemann, Anand Srivastav, Christian Schielke, Thorsten B. Reusch and Philip Rosenstiel

    BMC Bioinformatics 2017 18:324

    Published on: 3 July 2017

  11. Software

    SLMSuite: a suite of algorithms for segmenting genomic profiles

    The identification of copy number variants (CNVs) is essential to study human genetic variation and to understand the genetic basis of mendelian disorders and cancers. At present, genome-wide detection of CNVs...

    Valerio Orlandini, Aldesia Provenzano, Sabrina Giglio and Alberto Magi

    BMC Bioinformatics 2017 18:321

    Published on: 28 June 2017

  12. Methodology Article

    Quasi-linear score for capturing heterogeneous structure in biomarkers

    Linear scores are widely used to predict dichotomous outcomes in biomedical studies because of their learnability and understandability. Such approaches, however, cannot be used to elucidate biodiversity when ...

    Katsuhiro Omae, Osamu Komori and Shinto Eguchi

    BMC Bioinformatics 2017 18:308

    Published on: 19 June 2017

  13. Research article

    Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences

    DNA-binding proteins perform important functions in a great number of biological activities. DNA-binding proteins can interact with ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA), and DNA-binding p...

    Wei Wang, Lin Sun, Shiguang Zhang, Hongjun Zhang, Jinling Shi, Tianhe Xu and Keliang Li

    BMC Bioinformatics 2017 18:300

    Published on: 12 June 2017

  14. Software

    NaviSE: superenhancer navigator integrating epigenomics signal algebra

    Superenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration. Although there are pipeli...

    Alex M. Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta and Marcos J. Araúzo-Bravo

    BMC Bioinformatics 2017 18:296

    Published on: 6 June 2017

Previous Page Page 1 of 18 Next Page