Piet 0.1.0 – DNA CNV Analysis tools based on fused Lasso type of Model

Piet 0.1.0

:: DESCRIPTION

Piet provides some segmentation tools, using fused lasso, group fused lasso and generalized fused lasso (GFL), for analysis of individual or multiple sequences of CNV data.

::DEVELOPER

Piet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX / Linux
  • R package

:: DOWNLOAD

 Piet

:: MORE INFORMATION

Citation

Z. Zhang, K. Lange, C. Sabatti (2012)
Reconstructing DNA copy number by joint segmentation of multiple sequences

DiNAMO 1.0 – Discriminative DNA IUPAC motif discovery tool

DiNAMO 1.0

:: DESCRIPTION

The DiNAMO software implements an exhaustive algorithm to detect over-represented IUPAC motifs in a set of DNA sequences. It has two modes: scanning mode, where all windows are parsed, or fixed-position mode, where only motifs occurring at a specific position in the sequences are taken into account.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

DiNAMO

:: MORE INFORMATION

Citation:

Saad C, Noé L, Richard H, Leclerc J, Buisine MP, Touzet H, Figeac M.
DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data.
BMC Bioinformatics. 2018 Jun 11;19(1):223. doi: 10.1186/s12859-018-2215-1. PMID: 29890948; PMCID: PMC5996464.

OMiMa – Identify Functional Motifs in DNA or Protein Sequences

OMiMa

:: DESCRIPTION

The OMiMa (the Optimized Mixture Markov model) System is a computational tool for identifying functional motifs in DNA or protein sequences. OMiMa System is based on the Optimized Mixture of Markov models that are able to incorporate most dependencies within a motif. Most important, OMiMa is capable to adjust model complexity according to motif dependency structures, so it can minimize model complexity without compromising prediction accuracy. OMiMa uses our fast Markov chain optimization method, the Directed Neighbor-Joining (DNJ), which makes OMiMa more computationally efficent.

::DEVELOPER

OMiMa team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OMiMa

:: MORE INFORMATION

Citation

Weichun Huang, David M Umbach, Uwe Ohler, Leping Li.
Optimized mixed Markov models for motif identification.
BMC Bioinformatics 2006, 7:279

Chromatin Cutter 1.00 – Simulates the distribution of DNA in a Gel Electrophoresis Study of Yeast Chromatin cut by Enzymes

Chromatin Cutter 1.00

:: DESCRIPTION

Chromatin Cutter simulates the distribution of DNA in a gel electrophoresis study of Yeast chromatin cut by enzymes. It lets you specify the fraction of nucleosomes that are unwrapped (wrapped ones have inaccessible DNA). It lets you specify the variance in the distribution of nucleosomes around their mean distance. It lets you specify the number of cuts per unit length (enzyme concentration). It plots the effects of these on the log number of base pairs, which matches the gel electrophoresis mass distribution.

::DEVELOPER

CISMM (Computer Integrated Systems for Microscopy and Manipulation)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Chromatin Cutter

:: MORE INFORMATION

HelixMC – Python-based Monte Carlo simulator for DNA/RNA duplexes

HelixMC

:: DESCRIPTION

HelixMC is a software package for Monte-Carlo (MC) simulations of DNA/RNA helices using the base-pair level model. It provides a powerful tool to understand the flexibility of DNA/RNA helices through numerical simualtions.

::DEVELOPER

Das Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX/ Windows
  • Python
  • Numpy
  • Matplotlib
  • C/C++ compiler

:: DOWNLOAD

 HelixMC

 :: MORE INFORMATION

Citation

PLoS Comput Biol. 2014 Aug 7;10(8):e1003756. doi: 10.1371/journal.pcbi.1003756. eCollection 2014.
Blind predictions of DNA and RNA tweezers experiments with force and torque.
Chou FC, Lipfert J, Das R

TfReg 5.3- Calculating DNA or RNA Melting Temperatures and Average Strand Openings

TfReg 5.3

:: DESCRIPTION

TfReg implements the calculation of Peyrard-Bishop style Hamiltonians to obtain some physical properties of DNA and RNA duplexes. The method uses the transfer matrix technique for the calculation of the classical partition function. Also, TfReg calculates the regression of experimental versus predicted melting temperatures using the equivalent melting index.

::DEVELOPER

Gerald Weber

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TfReg

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 15;29(10):1345-7. doi: 10.1093/bioinformatics/btt133. Epub 2013 Mar 16.
TfReg: calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models.
Weber G.

iDNA-Methyl – Identifying DNA Methylation Sites via Pseudo Trinucleotide Composition

iDNA-Methyl

:: DESCRIPTION

The web-server iDNA-Methyl is according to its genetic codes by combining its trinucleotide composition (TNC) and the pseudo amino acid components (PseAAC) of the protein translated from the DNA sample. And by means of the approach of optimizing training datasets for predicting DNA methylation sites. Rigorous cross-validations on a set of experiment-confirmed datasets have indicated that these new predictors remarkably outperformed their counterparts in the existing prediction methods

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition.
Liu Z, Xiao X, Qiu WR, Chou KC.
Anal Biochem. 2015 Jan 14. pii: S0003-2697(14)00569-7. doi: 10.1016/j.ab.2014.12.009.

DisoRDPbind – Prediction of RNA, DNA and Protein Binding Regions

DisoRDPbind

:: DESCRIPTION

DisoRDPbind predicts the RNA-, DNA-, and protein-binding residues located in the intrinsically disordered regions.

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder.
Peng Z, Kurgan L.
Nucleic Acids Res. 2015 Oct 15;43(18):e121. doi: 10.1093/nar/gkv585.

PutGaps Beta – DNA Gapped File from Amino Acid Alignment

PutGaps Beta

:: DESCRIPTION

PutGaps is a software to add gaps to a DNA alignment file based on its Amino Acid equivalent.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

PutGaps

:: MORE INFORMATION

Multi-VORFFIP / VORFFIP – Predicts protein-, peptide-, DNA- and RNA-binding sites in Proteins

Multi-VORFFIP / VORFFIP

:: DESCRIPTION

Multi-VORFFIP is a structure-based, machine learning, computational method designed to predict protein-protein, protein-peptide, protein-DNA and protein-RNA binding sites. M-VORFFIP integrates a wide and heterogeneous set of residue- and environment-based information using a two-step Random Forest ensemble classifier.

VORFFIP (Voronoi Random Forest Feedback Interface Predictor) is structure-based computational method for prediction of protein binding sites.

::DEVELOPER

 Bioinformatics Lab :: IBERS :: Aberystwyth University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 15;28(14):1845-50. doi: 10.1093/bioinformatics/bts269. Epub 2012 May 4.
A holistic in silico approach to predict functional sites in protein structures.
Segura J1, Jones PF, Fernandez-Fuentes N.

BMC Bioinformatics. 2011 Aug 23;12:352. doi: 10.1186/1471-2105-12-352.
Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams.
Segura J1, Jones PF, Fernandez-Fuentes N.