LSPR – Detect Periodic Expression Profiles in DNA Microarray Time-series data

LSPR

:: DESCRIPTION

LSPR is a Matlab package used to detect periodic expression profiles in DNA microarray time-series data.

::DEVELOPER

LSPR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • MatLab

:: DOWNLOAD

  LSPR

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 1;27(7):1023-5. doi: 10.1093/bioinformatics/btr041. Epub 2011 Feb 3.
LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data.
Yang R1, Zhang C, Su Z.

GATK 4.2.2.0 – Analysis Tools for Next-generation DNA Sequencers

GATK 4.2.2.0

:: DESCRIPTION

GATK (The Genome Analysis Toolkit) is a structured programming framework designed to enable the rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce. Since the GATK’s traversal engine encapsulates the complexity of efficiently accessing the next-generation sequencing data, researchers and developers are free to focus on their specific analysis algorithms. This not only vastly improves the productivity of developers, who can quickly write new analyses, but also results in tools that are efficient and robust, and can benefit from improvements to a common data management engine.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

GATK

:: MORE INFORMATION

Citation

Depristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ.
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Nature Genetics 43, 491–498 (2011) doi:10.1038/ng.806

ArtWonk v4.4.1740 – DNA to MIDI Converter

ArtWonk v4.4.1740

:: DESCRIPTION

ArtWonk produces music, visuals and wordplay based on generative algorithms you interactively create by connecting modules (graphical objects representing functions and processes) in real time, adjusting the parameters as you go, in a drag & drop environment especially designed to be fast to learn, fast to use.

Source material can be anything at all: Fractals, DNA, EEGs, EKGs, stock quotes, you name it. Built in data extraction reads data from virtually any source, and an extensive DNA editor opens mountains of public domain genetic sequences to explore.

Genetic Music From DNA and Protein

::DEVELOPER

John Dunn and Algorithmic Arts

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ArtWonk

:: MORE INFORMATION

Citation:

Peter Hamlin
ALGORITHMIC ARTSARTWONK 1.2 (WIN)
2004 issue of Electronic Musician Magazine.

do_x3dna 2018 – Analyze Fluctuations in DNA or RNA Structures in Molecular Dynamics Trajectories

do_x3dna 2018

:: DESCRIPTION

The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations.

::DEVELOPER

Rajendra Kumar

:: SCREENSHOTS

N/a

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • 3DNA

:: DOWNLOAD

 do_x3dna

:: MORE INFORMATION

Citation

do_x3dna: A tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations.
Kumar R, Grubmüller H.
Bioinformatics. 2015 Apr 2. pii: btv190.

StatAlign 3.4 – Bayesian Analysis of Protein, DNA and RNA Sequences

StatAlign 3.4

:: DESCRIPTION

StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.

::DEVELOPER

StatAlign team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsx
  • Java

 StatAlign

:: MORE INFORMATION

Citation

Aádám Novák, István Miklós, Rune Lyngsø and Jotun Hein
StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees
Bioinformatics (2008) 24 (20): 2403-2404.

Arunapuram P, Edvardsson I, Golden M, Anderson JW, Novák A, Sükösd Z, Hein J (2013)
StatAlign 2.0: Combining statistical alignment with RNA secondary structure prediction. 
Bioinformatics,2013 Mar 1;29(5):654-5. doi:10.1093/bioinformatics/btt025.

CpGassoc 2.60 – Analysis of DNA Methylation Microarray data

CpGassoc 2.60

:: DESCRIPTION

CpGassoc – An R Function for Analysis of DNA Methylation Microarray Data The analysis of DNA methylation data has recently garnered attention among researchers from a variety of backgrounds, due to the availability of high-throughput methylation microarrays. The number of CpG sites that can be analyzed is growing rapidly – for example, the latest Illumina Infinium BeadChip interrogates ~450,000 CpG sites. With the growing interest in DNA methylation and the growing volume of data analyzed, there is a need for software to perform these types of analyses.

::DEVELOPER

R Barfield <barfieldrichard8 at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

CpGassoc

:: MORE INFORMATION

Citation

R. T. Barfield et al.
CpGassoc – An R Function for Analysis of DNA Methylation Microarray Data.
American Society of Human Genetics/ICHG 2011

regshape v1.1 – DNA Shape-based Classifier for Regulatory Elements(R pkg)

regshape v1.1

:: DESCRIPTION

The regshape R package  provides a classifier for predicting whether a given oligonucleotide sequence (of length l bp, where l would typically vary from six to as high as 25 bp) is, or is not, a transcription factor (TF) binding site.

::DEVELOPER

The Ramsey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 regshape

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jun 30. pii: btv391
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.
Yang J, Ramsey SA.

BRB-ArrayTools 4.6.2 – Visualization & Analysis of DNA Microarray Gene Expression Data

BRB-ArrayTools 4.6.2

:: DESCRIPTION

BRB-ArrayTools is an integrated software package for the analysis of DNA microarray data.

BRB-ArrayTools contains utilities for processing expression data from multiple experiments, visualization of data, multidimensional scaling, clustering of genes and samples, and classification and prediction of samples. BRB-ArrayTools features drill-down linkage to NCBI databases using clone, GenBank, or UniGene identifiers, and drill-down linkage to the NetAffx database using Probeset ids.

::DEVELOPER

the Biometric Research Branch of the Division of Cancer Treatment & Diagnosis of the National Cancer Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BRB-ArrayTools

:: MORE INFORMATION

Citation

Analysis of gene expression data using BRB-ArrayTools.
Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y.
Cancer Inform. 2007 Feb 4;3:11-7.

RiboSketch 0.8.2 – Visualization of multi-stranded RNA and DNA Secondary Structure

RiboSketch 0.8.2

:: DESCRIPTION

RiboSketch is a drawing program for the production of RNA and DNA secondary structure images.The user provides an input file (.ct, .bpseq, .dbn, or the save file type .rs) containing the sequence and base-pairing of the strand(s).

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

RiboSketch

:: MORE INFORMATION

Citation:

Lu JS, Bindewald E, Kasprzak WK, Shapiro BA.
RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure.
Bioinformatics. 2018 Dec 15;34(24):4297-4299. doi: 10.1093/bioinformatics/bty468. PMID: 29912310; PMCID: PMC6289134.

DDNA 3.1 – DNA/Protein Complex Interaction Energy

DDNA 3.1

:: DESCRIPTION

DDNA is a software for interaction energy between protein and DNA

::DEVELOPER

Laboratory of Structural Bioinformatics and Design

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DDNA

 :: MORE INFORMATION

Citation

Bioinformatics. 2010 Aug 1;26(15):1857-63. doi: 10.1093/bioinformatics/btq295. Epub 2010 Jun 4.
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function.
Zhao H1, Yang Y, Zhou Y.