:: DESCRIPTION
srnaloop searchs long DNA/RNA strings for small RNA hairpin loops that may be candidates for small RNA regulatory sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Cell. 2003 May;11(5):1253-63.
Computational and experimental identification of C. elegans microRNAs.
Grad Y1, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J.
:: DESCRIPTION
DNAFSMiner is a web-based software toolbox that aims to predict these functional sites in DNA sequences.Currently, there are two software tools. One is called TIS Miner which can be used to predict translation initiation site (TIS) in vertebrate mRNA, cDNA, or DNA sequences. The other is called Poly(A) Signal Miner which can be used to predict polyadenylation (poly(A)) signal in human DNA sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2005 Mar 1;21(5):671-3. Epub 2004 Jul 29.
DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences.
Liu H1, Han H, Li J, Wong L.
:: DESCRIPTION
iMolview is an app for the iPhone , iPad and Android that lets you browse protein, DNA, and drug molecules in 3D. The app has a direct link to the Protein Data Bank (PDB) and DrugBank and has a fast and easy to use interface. Touching the molecules via the screen allows you to interact immediately with the 3D structures in a unique way. You can zoom in and out, rotate, spin, pan, and clip the 3D molecules with your finger tips in ways that are impossible using a traditional mouse and desktop computer.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
BLAT (BLAST -like alignment tool) is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kent, W.J. 2002.
BLAT — The BLAST-Like Alignment Tool.
Genome Research 4: 656-664
:: DESCRIPTION
PhyloGibbs-MP is a motif finder to find binding sites for transcription factors in cis-regulatory sequences of DNA.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Rahul Siddharthan,
“PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling“,
PLoS Comput Biol 4(8): e1000156 (2008)
:: DESCRIPTION
LSPR is a Matlab package used to detect periodic expression profiles in DNA microarray time-series data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: 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
:: 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
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Peter Hamlin
ALGORITHMIC ARTSARTWONK 1.2 (WIN)
2004 issue of Electronic Musician Magazine.
:: DESCRIPTION
The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations.
::DEVELOPER
:: SCREENSHOTS
N/a
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: 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.