DECIPHER 2.20.0 – Decipher & Manage DNA Sequences

DECIPHER 2.20.0

:: DESCRIPTION

DECIPHER (Database Enabled Code for Ideal Probe Hybridization Employing R) is a software toolset that can be used for deciphering and managing DNA sequences efficiently using the R statistical programming language. The program is designed to be used with non-destructive workflows that guide the user through the process of importing, maintaining, analyzing, manipulating, and exporting a massive amount of DNA sequences.

::DEVELOPER

Erik Wright

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R package
BioConductor

:: DOWNLOAD

DECIPHER

:: MORE INFORMATION

Citation

DesignSignatures: a tool for designing primers that yield amplicons with distinct signatures.
Wright ES, Vetsigian KH.
Bioinformatics. 2016 Jan 23. pii: btw047

ES Wright et al. (2011)
“DECIPHER: A Search-Based Approach to Chimera Identification for 16S rRNA Sequences.”
Applied and Environmental Microbiology,

DanQ – A Hybrid Convolutional and Recurrent Neural Network for predicting the function of DNA Sequences

DanQ

:: DESCRIPTION

DanQ is a hybrid convolutional and recurrent neural network model for predicting the function of DNA de novo from sequence.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

DanQ

:: MORE INFORMATION

Citation

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
Quang D, Xie X.
Nucleic Acids Res. 2016 Apr 15. pii: gkw226.

ACT 13 – Display Pairwise Comparisons between DNA Sequences

ACT 13

:: DESCRIPTION

ACT ( Artemis Comparison Tool) is a free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation.

::DEVELOPER

the Sanger Institute

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java

:: DOWNLOAD

ACT

:: MORE INFORMATION

Citation

Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG and Parkhill J
ACT: the Artemis Comparison Tool.
Bioinformatics (Oxford, England) 2005;21;16;3422-3

mreps 2.6 – Detect Tandem Repeats in DNA sequences

mreps 2.6

:: DESCRIPTION

mreps is a flexible and efficient software for identifying serial repeats (usually called tandem repeats) in DNA sequences.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX

:: DOWNLOAD

mreps

:: MORE INFORMATION

Citation:

R. Kolpakov, G. Bana, and G. Kucherov,
mreps: efficient and flexible detection of tandem repeats in DNA,
Nucleic Acid Research, 31 (13), July 1 2003, pp 3672-3678.

TFM-Scan – Efficient Location of Position Weight Matrices on a DNA sequence

TFM-Scan

:: DESCRIPTION

TFM-Scan is a program dedicated to the location of large sets of putative transcription factor binding sites on a DNA sequence.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX/Windows
C++ Compiler

TFM-Scan

:: MORE INFORMATION

Citation

Large scale matching for Position Weight Matrices
Liefooghe A., Touzet H. and Varré J.-S.
In Combinatorial Pattern Matching, volume 4009 of Lecture Notes in Computer Science, pages 401-412. Springer Verlag, 2006.

Xpresso – Predicting Gene Expression levels from DNA Sequences

Xpresso

:: DESCRIPTION

Xpresso is a software suite whose goal is to predict gene expression levels and transcriptional activity from genomic sequences. It is trained using convolutional neural networks. Pre-trained models are available for the human, mouse, and several cell types for these species.

::DEVELOPER

Shendure Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows
Python
R

:: DOWNLOAD

Xpresso

:: MORE INFORMATION

Citation

Agarwal V, Shendure J.
Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks.
Cell Rep. 2020 May 19;31(7):107663. doi: 10.1016/j.celrep.2020.107663. PMID: 32433972.

XMatchView 1.2.5 – Visualize DNA Sequence Alignments.

XMatchView 1.2.5

:: DESCRIPTION

XMatchView is a python application designed to visualize DNA sequence alignments.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

:: REQUIREMENTS

Linux/Windows/MacOsX
Python

:: DOWNLOAD

XMatchView

:: MORE INFORMATION

AhoPro – Seach for Overrepresentation of Given motifs in DNA sequences, P-value calculation

AhoPro

:: DESCRIPTION

The project AhoPro was created to seach for overrepresentation of given motifs in DNA sequences and to search for motif cooccurrence. This could discover the synergy of transcription factors (TF), which usually takes place in regulatory modules of genes.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

WIndows

:: DOWNLOAD

AhoPro

:: MORE INFORMATION

Citation:

Algorithms Mol Biol. 2007 Oct 10;2:13.
Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.
Boeva V, Clément J, Régnier M, Roytberg MA, Makeev VJ.

Staden 2.0.0b11 – DNA Sequence Assembly , Editing and Analysis

Staden 2.0.0b11

:: DESCRIPTION

Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) .

::DEVELOPER

Staden Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX

:: DOWNLOAD

Staden

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jul 15;26(14):1699-703. doi: 10.1093/bioinformatics/btq268. Epub 2010 May 30.
Gap5–editing the billion fragment sequence assembly.
Bonfield JK1, Whitwham A.

Rodger Staden, David P. Judge and James K. Bonfield.
Analysing Sequences Using the Staden Package and EMBOSS.
Introduction to Bioinformatics. A Theoretical and Practical Approach. Eds. Stephen A. Krawetz and David D. Womble. Human Press Inc., Totawa, NJ 07512 (2003)

N-score – Predict Nucleosome Positions from DNA Sequence information

N-score

:: DESCRIPTION

N-score is a wavelet analysis based model for predicting nucleosome positions from DNA sequence information.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
Python/Matlab

:: DOWNLOAD

N-score

:: MORE INFORMATION

Citation

Genomic sequence is highly predictive of local nucleosome depletion.
Yuan GC, Liu JS.
PLoS Comput Biol. 2008 Jan;4(1):e13