Skip to content


BMC Bioinformatics

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 20 Next Page
  1. Content type: Software

    Prioritization of sequence variants for diagnosis and discovery of Mendelian diseases is challenging, especially in large collections of whole genome sequences (WGS). Fast, scalable solutions are needed for di...

    Authors: Steven Flygare, Edgar Javier Hernandez, Lon Phan, Barry Moore, Man Li, Anthony Fejes, Hao Hu, Karen Eilbeck, Chad Huff, Lynn Jorde, Martin G. Reese and Mark Yandell

    Citation: BMC Bioinformatics 2018 19:57

    Published on:

  2. Content type: Software

    The function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been developed to predict such structures or to use them to functionally a...

    Authors: Raúl Arias-Carrasco, Yessenia Vásquez-Morán, Helder I. Nakaya and Vinicius Maracaja-Coutinho

    Citation: BMC Bioinformatics 2018 19:55

    Published on:

  3. Content type: Methodology Article

    Long read sequencing is changing the landscape of genomic research, especially de novo assembly. Despite the high error rate inherent to long read technologies, increased read lengths dramatically improve the con...

    Authors: Jeremy R. Wang, James Holt, Leonard McMillan and Corbin D. Jones

    Citation: BMC Bioinformatics 2018 19:50

    Published on:

  4. Content type: Software

    Over the last few decades, computational genomics has tremendously contributed to decipher biology from genome sequences and related data. Considerable effort has been devoted to the prediction of transcriptio...

    Authors: Marco Di Salvo, Eva Pinatel, Adelfia Talà, Marco Fondi, Clelia Peano and Pietro Alifano

    Citation: BMC Bioinformatics 2018 19:36

    Published on:

  5. Content type: Software

    Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use ...

    Authors: David E. Condon, Phu V. Tran, Yu-Chin Lien, Jonathan Schug, Michael K. Georgieff, Rebecca A. Simmons and Kyoung-Jae Won

    Citation: BMC Bioinformatics 2018 19:31

    Published on:

  6. Content type: Software

    Genomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based ...

    Authors: Eliot C. Bush, Anne E. Clark, Carissa A. DeRanek, Alexander Eng, Juliet Forman, Kevin Heath, Alexander B. Lee, Daniel M. Stoebel, Zunyan Wang, Matthew Wilber and Helen Wu

    Citation: BMC Bioinformatics 2018 19:32

    Published on:

  7. Content type: Software

    GenIO is a novel web-server, designed to assist clinical genomics researchers and medical doctors in the diagnostic process of rare genetic diseases. The tool identifies the most probable variants causing a ra...

    Authors: Daniel Koile, Marta Cordoba, Maximiliano de Sousa Serro, Marcelo Andres Kauffman and Patricio Yankilevich

    Citation: BMC Bioinformatics 2018 19:25

    Published on:

  8. Content type: Research Article

    The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity...

    Authors: Guido Zampieri, Dinh Van Tran, Michele Donini, Nicolò Navarin, Fabio Aiolli, Alessandro Sperduti and Giorgio Valle

    Citation: BMC Bioinformatics 2018 19:23

    Published on:

  9. Content type: Methodology article

    Cluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing “outliers” among...

    Authors: Min Wang, Zachary B. Abrams, Steven M. Kornblau and Kevin R. Coombes

    Citation: BMC Bioinformatics 2018 19:9

    Published on:

  10. Content type: Research Article

    Genomic imprinting is one of the well-known epigenetic factors causing the association between traits and genes, and has generally been examined by detecting parent-of-origin effects of alleles. A lot of metho...

    Authors: Qi-Lei Zou, Xiao-Ping You, Jian-Long Li, Wing Kam Fung and Ji-Yuan Zhou

    Citation: BMC Bioinformatics 2018 19:8

    Published on:

  11. Content type: Methodology Article

    ‘Next-generation’ (NGS) sequencing has wide application in medical genetics, including the detection of somatic variation in cancer. The Ion Torrent-based (IONT) platform is among NGS technologies employed in ...

    Authors: Aditya Deshpande, Wenhua Lang, Tina McDowell, Smruthy Sivakumar, Jiexin Zhang, Jing Wang, F. Anthony San Lucas, Jerry Fowler, Humam Kadara and Paul Scheet

    Citation: BMC Bioinformatics 2018 19:5

    Published on:

  12. Content type: Software

    De novo prediction of Transcription Factor Binding Sites (TFBS) using computational methods is a difficult task and it is an important problem in Bioinformatics. The correct recognition of TFBS plays an important...

    Authors: Jader M. Caldonazzo Garbelini, André Y. Kashiwabara and Danilo S. Sanches

    Citation: BMC Bioinformatics 2018 19:4

    Published on:

  13. Content type: Methodology article

    Genotyping-by-sequencing (GBS), a method to identify genetic variants and quickly genotype samples, reduces genome complexity by using restriction enzymes to divide the genome into fragments whose ends are seq...

    Authors: Daniel P. Wickland, Gopal Battu, Karen A. Hudson, Brian W. Diers and Matthew E. Hudson

    Citation: BMC Bioinformatics 2017 18:586

    Published on:

  14. Content type: Research Article

    The next generation sequencing (NGS) techniques have been around for over a decade. Many of their fundamental applications rely on the ability to compute good genome assemblies. As the technology evolves, the ...

    Authors: Nilesh Khiste and Lucian Ilie

    Citation: BMC Bioinformatics 2017 18:564

    Published on:

  15. Content type: Methodology Article

    The spatial Principal Component Analysis (sPCA, Jombart (Heredity 101:92-103, 2008) is designed to investigate non-random spatial distributions of genetic variation. Unfortunately, the associated tests used fo...

    Authors: V. Montano and T. Jombart

    Citation: BMC Bioinformatics 2017 18:562

    Published on:

Previous Page Page 1 of 20 Next Page

2016 Journal Metrics

  • Citation Impact
    2.448 - 2-year Impact Factor
    3.450 - 5-year Impact Factor
    0.946 - Source Normalized Impact per Paper (SNIP)
    1.467 - SCImago Journal Rank (SJR)

    1405 Usage Factor

    Social Media Impact
    816 mentions