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Sequence analysis (applications)

Section edited by João Setubal

This section incorporates all aspects of sequence analysis applications, including but not limited to: software, workflows and webservers dealing with applied sequence/genome analysis, sequence assembly, analysis of sequence features, and protein function and ligand binding, estimated through sequence features.

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  1. Short oligonucleotides can be used as markers to tag and track DNA sequences. For example, barcoding techniques (i.e. Multiplex Identifiers or Indexing) use short oligonucleotides to distinguish between reads fro...

    Authors: Scott M Yourstone, Derek S Lundberg, Jeffery L Dangl and Corbin D Jones

    Citation: BMC Bioinformatics 2014 15:284

    Content type: Software

    Published on:

  2. UniFrac is a well-known tool for comparing microbial communities and assessing statistically significant differences between communities. In this paper we identify a discrepancy in the UniFrac methodology that...

    Authors: Jeffrey R Long, Vanessa Pittet, Brett Trost, Qingxiang Yan, David Vickers, Monique Haakensen and Anthony Kusalik

    Citation: BMC Bioinformatics 2014 15:278

    Content type: Correspondence

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  3. Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep...

    Authors: Jiyuan An, John Lai, Atul Sajjanhar, Melanie L Lehman and Colleen C Nelson

    Citation: BMC Bioinformatics 2014 15:275

    Content type: Software

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  4. The use of sequencing technologies to investigate the microbiome of a sample can positively impact patient healthcare by providing therapeutic targets for personalized disease treatment. However, these samples...

    Authors: Allyson L Byrd, Joseph F Perez-Rogers, Solaiappan Manimaran, Eduardo Castro-Nallar, Ian Toma, Tim McCaffrey, Marc Siegel, Gary Benson, Keith A Crandall and William Evan Johnson

    Citation: BMC Bioinformatics 2014 15:262

    Content type: Methodology article

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  5. Chickpea (Cicer arietinum) is a widely grown legume crop in tropical, sub-tropical and temperate regions. Molecular breeding approaches seem to be essential for enhancing crop productivity in chickpea. Until rece...

    Authors: Dadakhalandar Doddamani, Mohan AVSK Katta, Aamir W Khan, Gaurav Agarwal, Trushar M Shah and Rajeev K Varshney

    Citation: BMC Bioinformatics 2014 15:212

    Content type: Database

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  6. Detection of large genomic rearrangements, such as large indels, duplications or translocations is now commonly achieved by next generation sequencing (NGS) approaches. Recently, several tools have been develo...

    Authors: Delphine Naquin, Yves d’Aubenton-Carafa, Claude Thermes and Maud Silvain

    Citation: BMC Bioinformatics 2014 15:198

    Content type: Software

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  7. Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for query...

    Authors: Sean R Wilkinson and Jonas S Almeida

    Citation: BMC Bioinformatics 2014 15:176

    Content type: Research article

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  8. Gene expression in vertebrate cells may be controlled post-transcriptionally through regulatory elements in mRNAs. These are usually located in the untranslated regions (UTRs) of mRNA sequences, particularly t...

    Authors: Ambarish Biswas and Chris M Brown

    Citation: BMC Bioinformatics 2014 15:174

    Content type: Software

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  9. Several methods are available for the detection of covarying positions from a multiple sequence alignment (MSA). If the MSA contains a large number of sequences, information about the proximities between resid...

    Authors: Greg W Clark, Sharon H Ackerman, Elisabeth R Tillier and Domenico L Gatti

    Citation: BMC Bioinformatics 2014 15:157

    Content type: Methodology article

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  10. Accurate somatic mutation-calling is essential for insightful mutation analyses in cancer studies. Several mutation-callers are publicly available and more are likely to appear. Nonetheless, mutation-calling i...

    Authors: Su Yeon Kim, Laurent Jacob and Terence P Speed

    Citation: BMC Bioinformatics 2014 15:154

    Content type: Research article

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  11. Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-ca...

    Authors: Filip Bielejec, Philippe Lemey, Luiz Max Carvalho, Guy Baele, Andrew Rambaut and Marc A Suchard

    Citation: BMC Bioinformatics 2014 15:133

    Content type: Software

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  12. Current-generation sequencing technologies are able to produce low-cost, high-throughput reads. However, the produced reads are imperfect and may contain various sequencing errors. Although many error correcti...

    Authors: Adrianto Wirawan, Robert S Harris, Yongchao Liu, Bertil Schmidt and Jan Schröder

    Citation: BMC Bioinformatics 2014 15:131

    Content type: Methodology article

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  13. Advances in sequencing efficiency have vastly increased the sizes of biological sequence databases, including many thousands of genome-sequenced species. The BLAST algorithm remains the main search engine for ...

    Authors: Ralf Stefan Neumann, Surendra Kumar, Thomas Hendricus Augustus Haverkamp and Kamran Shalchian-Tabrizi

    Citation: BMC Bioinformatics 2014 15:128

    Content type: Software

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  14. The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to ...

    Authors: Sergey Koren, Todd J Treangen, Christopher M Hill, Mihai Pop and Adam M Phillippy

    Citation: BMC Bioinformatics 2014 15:126

    Content type: Software

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  15. Genotypes generated in next generation sequencing studies contain errors which can significantly impact the power to detect signals in common and rare variant association tests. These genotyping errors are not...

    Authors: Andrew R Carson, Erin N Smith, Hiroko Matsui, Sigrid K Brækkan, Kristen Jepsen, John-Bjarne Hansen and Kelly A Frazer

    Citation: BMC Bioinformatics 2014 15:125

    Content type: Methodology article

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  16. Small insertion and deletion polymorphisms (Indels) are the second most common mutations in the human genome, after Single Nucleotide Polymorphisms (SNPs). Recent studies have shown that they have significant ...

    Authors: Carlos Bermejo-Das-Neves, Hoan-Ngoc Nguyen, Olivier Poch and Julie D Thompson

    Citation: BMC Bioinformatics 2014 15:111

    Content type: Research article

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  17. Tuberculosis is an infectious bacterial disease caused by Mycobacterium tuberculosis. It remains a major health threat, killing over one million people every year worldwide. An early antibiotic therapy is the bas...

    Authors: Jean-Pierre Flandrois, Gérard Lina and Oana Dumitrescu

    Citation: BMC Bioinformatics 2014 15:107

    Content type: Database

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  18. Amino acid sequences and features extracted from such sequences have been used to predict many protein properties, such as subcellular localization or solubility, using classifier algorithms. Although software...

    Authors: Bastiaan A van den Berg, Marcel JT Reinders, Johannes A Roubos and Dick de Ridder

    Citation: BMC Bioinformatics 2014 15:93

    Content type: Software

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  19. 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein...

    Authors: László Kaján, Thomas A Hopf, Matúš Kalaš, Debora S Marks and Burkhard Rost

    Citation: BMC Bioinformatics 2014 15:85

    Content type: Software

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  20. Chromothripsis, a newly discovered type of complex genomic rearrangement, has been implicated in the evolution of several types of cancers. To date, it has been described in bone cancer, SHH-medulloblastoma an...

    Authors: Shaylan K Govind, Amin Zia, Pablo H Hennings-Yeomans, John D Watson, Michael Fraser, Catalina Anghel, Alexander W Wyatt, Theodorus van der Kwast, Colin C Collins, John D McPherson, Robert G Bristow and Paul C Boutros

    Citation: BMC Bioinformatics 2014 15:78

    Content type: Software

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  21. Metagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities. Following recent advances i...

    Authors: Simon Roux, Jeremy Tournayre, Antoine Mahul, Didier Debroas and François Enault

    Citation: BMC Bioinformatics 2014 15:76

    Content type: Software

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  22. The correlations of genotypic and phenotypic tests with treatment, clinical history and the significance of mutations in viruses of HIV-infected patients are used to establish resistance mutations to protease ...

    Authors: Carlos Mata-Munguía, Martha Escoto-Delgadillo, Blanca Torres-Mendoza, Mario Flores-Soto, Mildred Vázquez-Torres, Francisco Gálvez-Gastelum, Arturo Viniegra-Osorio, Marcelo Castillero-Manzano and Eduardo Vázquez-Valls

    Citation: BMC Bioinformatics 2014 15:72

    Content type: Research article

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  23. Transposition event detection of transposable element (TE) in the genome using short reads from the next-generation sequence (NGS) was difficult, because the nucleotide sequence of TE itself is repetitive, mak...

    Authors: Mariko Nakagome, Elena Solovieva, Akira Takahashi, Hiroshi Yasue, Hirohiko Hirochika and Akio Miyao

    Citation: BMC Bioinformatics 2014 15:71

    Content type: Research article

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  24. As a fundamental genomic element, meiotic recombination hotspot plays important roles in life sciences. Thus uncovering its regulatory mechanisms has broad impact on biomedical research. Despite the recent ide...

    Authors: Peng Yang, Min Wu, Jing Guo, Chee Keong Kwoh, Teresa M Przytycka and Jie Zheng

    Citation: BMC Bioinformatics 2014 15:48

    Content type: Software

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  25. PSEUDOMARKER is a software package that performs joint linkage and linkage disequilibrium analysis between a marker and a putative disease locus. A key feature of PSEUDOMARKER is that it can combine case-contr...

    Authors: Edward Michael Gertz, Tero Hiekkalinna, Sébastien Le Digabel, Charles Audet, Joseph D Terwilliger and Alejandro A Schäffer

    Citation: BMC Bioinformatics 2014 15:47

    Content type: Software

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  26. Mixtures of internationally traded organic substances can contain parts of species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These mixtures often...

    Authors: Youri Lammers, Tamara Peelen, Rutger A Vos and Barbara Gravendeel

    Citation: BMC Bioinformatics 2014 15:44

    Content type: Software

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  27. The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for...

    Authors: Susan M Huse, David B Mark Welch, Andy Voorhis, Anna Shipunova, Hilary G Morrison, A Murat Eren and Mitchell L Sogin

    Citation: BMC Bioinformatics 2014 15:41

    Content type: Software

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  28. Several small open reading frames located within the 5′ untranslated regions of mRNAs have recently been shown to be translated. In humans, about 50% of mRNAs contain at least one upstream open reading frame r...

    Authors: Adam Skarshewski, Mitchell Stanton-Cook, Thomas Huber, Sumaya Al Mansoori, Ross Smith, Scott A Beatson and Joseph A Rothnagel

    Citation: BMC Bioinformatics 2014 15:36

    Content type: Software

    Published on:

  29. Automated gene-calling is still an error-prone process, particularly for the highly plastic genomes of fungal species. Improvement through quality control and manual curation of gene models is a time-consuming...

    Authors: Ate van der Burgt, Edouard Severing, Jérôme Collemare and Pierre JGM de Wit

    Citation: BMC Bioinformatics 2014 15:19

    Content type: Methodology article

    Published on:

  30. Information about genes, transcripts and proteins is spread over a wide variety of databases. Different tools have been developed using these databases to identify biological signals in gene lists from large s...

    Authors: Herbert Baier and Jörg Schultz

    Citation: BMC Bioinformatics 2014 15:18

    Content type: Software

    Published on:

  31. Logos are commonly used in molecular biology to provide a compact graphical representation of the conservation pattern of a set of sequences. They render the information contained in sequence alignments or pro...

    Authors: Travis J Wheeler, Jody Clements and Robert D Finn

    Citation: BMC Bioinformatics 2014 15:7

    Content type: Software

    Published on:

  32. Qualitative and quantitative analysis of small non-coding RNAs by next generation sequencing (smallRNA-Seq) represents a novel technology increasingly used to investigate with high sensitivity and specificity ...

    Authors: Giorgio Giurato, Maria Rosaria De Filippo, Antonio Rinaldi, Adnan Hashim, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo and Alessandro Weisz

    Citation: BMC Bioinformatics 2013 14:362

    Content type: Software

    Published on:

  33. DNA methylation is indispensible for normal human genome function. Currently there is an increasingly large number of DNA methylomic data being released in the public domain allowing for an opportunity to inve...

    Authors: Robert Lowe and Vardhman K Rakyan

    Citation: BMC Bioinformatics 2013 14:359

    Content type: Database

    Published on:

  34. Modern biological science generates a vast amount of data, the analysis of which presents a major challenge to researchers. Data are commonly represented in tables stored as plain text files and require line-b...

    Authors: Jerome Kelleher, Rob W Ness and Daniel L Halligan

    Citation: BMC Bioinformatics 2013 14:356

    Content type: Software

    Published on:

  35. Protein kinases are involved in relevant physiological functions and a broad number of mutations in this superfamily have been reported in the literature to affect protein function and stability. Unfortunately...

    Authors: Jose MG Izarzugaza, Miguel Vazquez, Angela del Pozo and Alfonso Valencia

    Citation: BMC Bioinformatics 2013 14:345

    Content type: Software

    Published on:

  36. Membrane transporters catalyze the transport of small solute molecules across biological barriers such as lipid bilayer membranes. Experimental identification of the transported substrates is very tedious. Onc...

    Authors: Ahmad Barghash and Volkhard Helms

    Citation: BMC Bioinformatics 2013 14:343

    Content type: Research article

    Published on:

  37. In the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source of protein-coding gene sequences, and have helped projects grow from a f...

    Authors: Casey W Dunn, Mark Howison and Felipe Zapata

    Citation: BMC Bioinformatics 2013 14:330

    Content type: Software

    Published on:

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