Literature DB >> 23132505

D-peaks: a visual tool to display ChIP-seq peaks along the genome.

Sylvain Brohée1, Gianluca Bontempi.   

Abstract

ChIP-sequencing is a method of choice to localize the positions of protein binding sites on DNA on a whole genomic scale. The deciphering of the sequencing data produced by this novel technique is challenging and it is achieved by their rigorous interpretation using dedicated tools and adapted visualization programs. Here, we present a bioinformatics tool (D-peaks) that adds several possibilities (including, user-friendliness, high-quality, relative position with respect to the genomic features) to the well-known visualization browsers or databases already existing. D-peaks is directly available through its web interface http://rsat.ulb.ac.be/dpeaks/ as well as a command line tool.

Entities:  

Keywords:  ChIPseq; bioinformatics; high-throughput sequencing; transcription factor; visualization

Mesh:

Substances:

Year:  2012        PMID: 23132505      PMCID: PMC3632623          DOI: 10.4161/trns.22457

Source DB:  PubMed          Journal:  Transcription        ISSN: 2154-1272


  8 in total

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4.  Evaluation of algorithm performance in ChIP-seq peak detection.

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5.  seqMINER: an integrated ChIP-seq data interpretation platform.

Authors:  Tao Ye; Arnaud R Krebs; Mohamed-Amin Choukrallah; Celine Keime; Frederic Plewniak; Irwin Davidson; Laszlo Tora
Journal:  Nucleic Acids Res       Date:  2010-12-21       Impact factor: 16.971

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Journal:  Nucleic Acids Res       Date:  2011-11-15       Impact factor: 16.971

7.  A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments.

Authors:  Teemu D Laajala; Sunil Raghav; Soile Tuomela; Riitta Lahesmaa; Tero Aittokallio; Laura L Elo
Journal:  BMC Genomics       Date:  2009-12-18       Impact factor: 3.969

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Journal:  Nature       Date:  2012-02-01       Impact factor: 49.962

  8 in total
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  1 in total

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