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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. Our current understanding of transcription factor binding sites (TFBSs) in sequenced prokaryotic genomes is very limited due to the lack of an accurate and efficient computational method for the prediction of ...

    Authors: Shaoqiang Zhang, Shan Li, Phuc T Pham and Zhengchang Su

    Citation: BMC Bioinformatics 2010 11:397

    Content type: Methodology article

    Published on:

  2. In the last decade, biochemical studies have revealed that epigenetic modifications including histone modifications, histone variants and DNA methylation form a complex network that regulate the state of chrom...

    Authors: Xiaojiang Xu, Stephen Hoang, Marty W Mayo and Stefan Bekiranov

    Citation: BMC Bioinformatics 2010 11:396

    Content type: Research article

    Published on:

  3. Microarray measurements are susceptible to a variety of experimental artifacts, some of which give rise to systematic biases that are spatially dependent in a unique way on each chip. It is likely that such ar...

    Authors: High Seng Chai, Terry M Therneau, Kent R Bailey and Jean-Pierre A Kocher

    Citation: BMC Bioinformatics 2010 11:356

    Content type: Methodology article

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  4. The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA seq...

    Authors: Liqun Xi, Yvonne Fondufe-Mittendorf, Lei Xia, Jared Flatow, Jonathan Widom and Ji-Ping Wang

    Citation: BMC Bioinformatics 2010 11:346

    Content type: Methodology article

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  5. Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many m...

    Authors: Jay Vyas, Ronald J Nowling, Thomas Meusburger, David Sargeant, Krishna Kadaveru, Michael R Gryk, Vamsi Kundeti, Sanguthevar Rajasekaran and Martin R Schiller

    Citation: BMC Bioinformatics 2010 11:328

    Content type: Software

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  6. Genome-wide association studies (GWAS) based on single nucleotide polymorphisms (SNPs) revolutionized our perception of the genetic regulation of complex traits and diseases. Copy number variations (CNVs) prom...

    Authors: Lukas Forer, Sebastian Schönherr, Hansi Weissensteiner, Florian Haider, Thomas Kluckner, Christian Gieger, Heinz-Erich Wichmann, Günther Specht, Florian Kronenberg and Anita Kloss-Brandstätter

    Citation: BMC Bioinformatics 2010 11:318

    Content type: Software

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  7. Whole genome association studies using highly dense single nucleotide polymorphisms (SNPs) are a set of methods to identify DNA markers associated with variation in a particular complex trait of interest. One ...

    Authors: Stephen J Goodswen, Cedric Gondro, Nathan S Watson-Haigh and Haja N Kadarmideen

    Citation: BMC Bioinformatics 2010 11:311

    Content type: Database

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  8. Guanosine triphosphate (GTP)-binding proteins play an important role in regulation of G-protein. Thus prediction of GTP interacting residues in a protein is one of the major challenges in the field of the comp...

    Authors: Jagat S Chauhan, Nitish K Mishra and Gajendra PS Raghava

    Citation: BMC Bioinformatics 2010 11:301

    Content type: Research article

    Published on:

  9. Position-specific priors have been shown to be a flexible and elegant way to extend the power of Gibbs sampler-based motif discovery algorithms. Information of many types–including sequence conservation, nucle...

    Authors: Timothy L Bailey, Mikael Bodén, Tom Whitington and Philip Machanick

    Citation: BMC Bioinformatics 2010 11:179

    Content type: Research article

    Published on:

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