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.

Pse-in-One 1.0.6 – Generating various modes of Pseudo Components of DNA, RNA and Protein Sequences

Pse-in-One 1.0.6

:: DESCRIPTION

Pse-in-One is a web server for generating various modes of pseudo components of DNA, RNA and protein sequences

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 Pse-in-One

:: MORE INFORMATION

Citation

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences.
Liu B, Liu F, Wang X, Chen J, Fang L, Chou KC.
Nucleic Acids Res. 2015 Jul 1;43(W1):W65-71. doi: 10.1093/nar/gkv458.

ADAPT 1.00 – Alignment of DNA Associated Profiles Tool

ADAPT 1.00

:: DESCRIPTION

ADAPT (Alignment of DNA Associated Profiles Tool)

::DEVELOPER

BioInformatics Group Mittweida

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 ADAPT

:: MORE INFORMATION

Citation:

Bussiek M, Labudde D, Beier R, Mücke N, Nellen W:
“Correlation of bending propensity profiles at Dictyostelium discoideum promoters with developmental transcription regulation.” 2013

Jolecule 2.0 – HTML5 Web-based Three-Dimensional Protein and DNA Renderer

Jolecule 2.0

:: DESCRIPTION

Jolecule is a HTML5 viewer for protein molecules. It is written in Javascript and is designed to be deployed on web pages. Jolecule provides a plugin mode that is meant to work in embedded in an arbitrary web page.

::DEVELOPER

Bosco Ho.

:: SCREENSHOTS

:: REQUIREMENTS

  • HTML5 suportted Web Browser 

:: DOWNLOAD

 Jolecule

:: MORE INFORMATION

Phred/Phrap/Consed 29.0 – DNA Sequence Assembler & Finishing Tools

Phred/Phrap/Consed 29.0

:: DESCRIPTION

Phred reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.

phrap is a program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets.

Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.

::DEVELOPER

Laboratory of PHIL GREEN

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Mac OsX

:: DOWNLOAD

Phred/Phrap/Consed

:: MORE INFORMATION

Citation:

KAnalyze 2.0.0 – DNA/RNA Sequence K-mer Toolkit

KAnalyze 2.0.0

:: DESCRIPTION

KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers.

::DEVELOPER

Vannberg Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 KAnalyze

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 18.
KAnalyze: A Fast Versatile Pipelined K-mer Toolkit.
Audano P1, Vannberg F.

tantan 22 – Find Cryptic Repeats in DNA, RNA, and Protein Sequences.

tantan 22

:: DESCRIPTION

tantan is a tool to mask simple regions (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences.The aim of tantan is to prevent false predictions when searching for homologous regions between two sequences. Simple repeats often align strongly to each other, causing false homology predictions.

::DEVELOPER

Martin C. Frith

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 tantan

:: MORE INFORMATION

Citation

MC Frith,
A new repeat-masking method enables specific detection of homologous sequences,
Nucleic Acids Research 2011 39(4):e23.