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. Research Article

    Meta-aligner: long-read alignment based on genome statistics

    Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducin...

    Damoon Nashta-ali, Ali Aliyari, Ahmad Ahmadian Moghadam, Mohammad Amin Edrisi, Seyed Abolfazl Motahari and Babak Hossein Khalaj

    BMC Bioinformatics 2017 18:126

    Published on: 23 February 2017

  2. Software

    TipMT: Identification of PCR-based taxon-specific markers

    Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attr...

    Gabriela F. Rodrigues-Luiz, Mariana S. Cardoso, Hugo O. Valdivia, Edward V. Ayala, Célia M. F. Gontijo, Thiago de S. Rodrigues, Ricardo T. Fujiwara, Robson S. Lopes and Daniella C. Bartholomeu

    BMC Bioinformatics 2017 18:104

    Published on: 11 February 2017

  3. Methodology article

    Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

    Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic p...

    O. Pipek, D. Ribli, J. Molnár, Á. Póti, M. Krzystanek, A. Bodor, G. E. Tusnády, Z. Szallasi, I. Csabai and D. Szüts

    BMC Bioinformatics 2017 18:73

    Published on: 31 January 2017

  4. Methodology Article

    Disorder recognition in clinical texts using multi-label structured SVM

    Information extraction in clinical texts enables medical workers to find out problems of patients faster as well as makes intelligent diagnosis possible in the future. There has been a lot of work about disord...

    Wutao Lin, Donghong Ji and Yanan Lu

    BMC Bioinformatics 2017 18:75

    Published on: 31 January 2017

  5. Methodology Article

    Eigen-Epistasis for detecting gene-gene interactions

    A large amount of research has been devoted to the detection and investigation of epistatic interactions in genome-wide association studies (GWASs). Most of the literature focuses on low-order interactions bet...

    Virginie Stanislas, Cyril Dalmasso and Christophe Ambroise

    BMC Bioinformatics 2017 18:54

    Published on: 23 January 2017

  6. Research Article

    Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers

    Next-generation sequencing of matched tumor and normal biopsy pairs has become a technology of paramount importance for precision cancer treatment. Sequencing costs have dropped tremendously, allowing the sequ...

    Ariane L. Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch and Niko Beerenwinkel

    BMC Bioinformatics 2017 18:8

    Published on: 3 January 2017

  7. Methodology article

    Negative binomial mixed models for analyzing microbiome count data

    Recent advances in next-generation sequencing (NGS) technology enable researchers to collect a large volume of metagenomic sequencing data. These data provide valuable resources for investigating interactions ...

    Xinyan Zhang, Himel Mallick, Zaixiang Tang, Lei Zhang, Xiangqin Cui, Andrew K. Benson and Nengjun Yi

    BMC Bioinformatics 2017 18:4

    Published on: 3 January 2017

  8. Software

    acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

    A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable qu...

    Markus Lux, Jan Krüger, Christian Rinke, Irena Maus, Andreas Schlüter, Tanja Woyke, Alexander Sczyrba and Barbara Hammer

    BMC Bioinformatics 2016 17:543

    Published on: 20 December 2016

  9. Research Article

    New tools to analyze overlapping coding regions

    Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop se...

    Amir H. Bayegan, Juan Antonio Garcia-Martin and Peter Clote

    BMC Bioinformatics 2016 17:530

    Published on: 13 December 2016

  10. Research article

    Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations

    Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedl...

    Camilo Andrés Mora Osorio and Andrés Fernando González Barrios

    BMC Bioinformatics 2016 17:522

    Published on: 7 December 2016

  11. Research article

    Predicting the recurrence of noncoding regulatory mutations in cancer

    One of the greatest challenges in cancer genomics is to distinguish driver mutations from passenger mutations. Whereas recurrence is a hallmark of driver mutations, it is difficult to observe recurring noncodi...

    Woojin Yang, Hyoeun Bang, Kiwon Jang, Min Kyung Sung and Jung Kyoon Choi

    BMC Bioinformatics 2016 17:492

    Published on: 3 December 2016

  12. Software

    ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons

    CpG sites in an individual molecule may exist in a binary state (methylated or unmethylated) and each individual DNA molecule, containing a certain number of CpGs, is a combination of these states defining an ...

    Giovanni Scala, Ornella Affinito, Domenico Palumbo, Ermanno Florio, Antonella Monticelli, Gennaro Miele, Lorenzo Chiariotti and Sergio Cocozza

    BMC Bioinformatics 2016 17:484

    Published on: 25 November 2016

  13. Software

    muBLASTP: database-indexed protein sequence search on multicore CPUs

    The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utili...

    Jing Zhang, Sanchit Misra, Hao Wang and Wu-chun Feng

    BMC Bioinformatics 2016 17:443

    Published on: 4 November 2016

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