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.

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  1. Software

    VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data

    Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perfor...

    Scott Christley, Mikhail K. Levin, Inimary T. Toby, John M. Fonner, Nancy L. Monson, William H. Rounds, Florian Rubelt, Walter Scarborough, Richard H. Scheuermann and Lindsay G. Cowell

    BMC Bioinformatics 2017 18:448

    Published on: 11 October 2017

  2. Methodology Article

    Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae

    Geminiviruses infect a broad range of cultivated and non-cultivated plants, causing significant economic losses worldwide. The studies of the diversity of species, taxonomy, mechanisms of evolution, geographic...

    José Cleydson F. Silva, Thales F. M. Carvalho, Elizabeth P. B. Fontes and Fabio R. Cerqueira

    BMC Bioinformatics 2017 18:431

    Published on: 30 September 2017

  3. Software

    Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling

    Elaboration of powerful methods to predict functional and/or physical protein-protein interactions from genome sequence is one of the main tasks in the post-genomic era. Phylogenetic profiling allows the predi...

    Gabriella Sferra, Federica Fratini, Marta Ponzi and Elisabetta Pizzi

    BMC Bioinformatics 2017 18:396

    Published on: 5 September 2017

  4. Methodology Article

    A weighted string kernel for protein fold recognition

    Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done bef...

    Saghi Nojoomi and Patrice Koehl

    BMC Bioinformatics 2017 18:378

    Published on: 25 August 2017

  5. Methodology Article

    Identifying pleiotropic genes in genome-wide association studies from related subjects using the linear mixed model and Fisher combination function

    A multivariate genome-wide association test is proposed for analyzing data on multivariate quantitative phenotypes collected from related subjects. The proposed method is a two-step approach. The first step mo...

    James J. Yang, L Keoki Williams and Anne Buu

    BMC Bioinformatics 2017 18:376

    Published on: 24 August 2017

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

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