RIPCAL 2.0 – Analysis of RIP in Fungal Genomic DNA Repeats

RIPCAL 2.0

:: DESCRIPTION

RIPCAL is a bioinformatics tool for the analysis of repeat-induced point mutation (RIP) of fungi.

::DEVELOPER

Dr James Hane

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl
:: DOWNLOAD

 RIPCAL

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Nov 24;11:655. doi: 10.1186/1471-2164-11-655.
In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes.
Hane JK1, Oliver RP.

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences.
Hane JK, Oliver RP.
BMC Bioinformatics. 2008 Nov 12;9:478. doi: 10.1186/1471-2105-9-478.

RIPSeeker 1.26.0 – de novo RIP Peak Predictions based on HMM.

RIPSeeker 1.26.0

:: DESCRIPTION

RIPSeeker is a free open-source Bioconductor/R package for identifying protein-associated transcripts from RIP-seq experiments.

::DEVELOPER

Yue Li @ The Zhang Lab, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 RIPSeeker

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Apr;41(8):e94. doi: 10.1093/nar/gkt142. Epub 2013 Feb 28.
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.
Li Y1, Zhao DY, Greenblatt JF, Zhang Z.

RIP 1.1 – Predicting Target Genes of Transcription Factors

RIP 1.1

:: DESCRIPTION

RIP (regulatory interaction predictor) is a machine learning approach that inferred 73,923 RIs for 301 human TFs and 11,263 target genes with considerably good quality and 4,516 RIs with very high quality. The inference of RIs is independent of any specific condition.

::DEVELOPER

EILSLABS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • R package

:: DOWNLOAD

 RIP

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 15;27(16):2239-47. doi: 10.1093/bioinformatics/btr366. Epub 2011 Jun 20.
RIP: the regulatory interaction predictor–a machine learning-based approach for predicting target genes of transcription factors.
Bauer T, Eils R, König R.

RIP 1.1 – Accelerated Molecular Dynamics

RIP 1.1

:: DESCRIPTION

RIP (Rotamerically Induced Perturbation) generates local perturbations of residues in a protein. In picoseconds of a molecular-dynamics (MD) simulation, RIP generates motions that reveal certain mechanical properties of a protein. 1) Flexibility Analysis: using larger perturbations, RIP can induce several ?ngstroms of conformational change in loops, identifying potential allosteric effectors. E.g. on the right is the RIP perturbation on TRP-83 in the Ligand-Binding Domain of the Estrogen Receptor, which produces a dramatic 10 ? motion of the ligand-binding Helix 12 in a 10 ps simulation. 2) Coupling Analysis: using small RIP perturbations, residues that interact strongly can be identified. Analysis of the patterns of strongly interacting residues allows an analysis of tertiary structure dynamics.

::DEVELOPER

Bosco K. Ho

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

RIP

:: MORE INFORMATION

Reference for Flexibility Analysis: “Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations” by Bosco K. Ho and David A. Agard. PLoS Comput Biol (2009) 5(4): e1000343.

Reference for Coupling Analysis: “Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility“by Bosco K. Ho and David A. Agard. Protein Science (2010) 19:398-411.

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