draw+sneakpeek – DNA Resequencing Analysis Workflow

draw+sneakpeek

:: DESCRIPTION

DRAW and SneakPeek are two computer programs that we use for analyzing whole-genome and whole-exome DNA-seq experiments.

DRAW stands for DNA Resequencing Analysis Workflow. DRAW automates the entire process of mapping sequence reads, various quality control steps and calling variants.

SneakPeek is a web-based diagnostic tool for reviewing quality metrics generated by our DNA Resequencing Analysis Workflow (DRAW).

::DEVELOPER

 Wang Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Amazon EC2 / Linux

:: DOWNLOAD

 draw+sneakpeek

:: MORE INFORMATION

Citation

Lin CF, Valladares O, Childress DM, Klevak E, Geller ET, Hwang YC, Tsai EA, Schellenberg GD, and Wang LS.
DRAW+SneakPeek: Analysis Workflow and Quality Metric Man-agement for DNA-Seq Experiments.
Bioinformatics (2013) 29 (19): 2498-2500. doi: 10.1093/bioinformatics/btt422

Unrooted – Draw Binary Tree Expressed in the standard Phylogenetic Tree Format

Unrooted

:: DESCRIPTION

Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). Trees are drawn in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches.

::DEVELOPER

Unrooted team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows

:: DOWNLOAD

 Unrooted

:: MORE INFORMATION

KegDraw 0.1.15 beta – Draw Compound & Glycan Structures

KegDraw 0.1.15 beta

:: DESCRIPTION

KegDraw is a java application for drawing compound and glycan structures with capabilities to search against the KEGG databases.

::DEVELOPER

Kanehisa Laboratories

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

KegDraw

:: MORE INFORMATION

Citation

Glycobiology. 2006 May;16(5):63R-70R. Epub 2005 Jul 13.
KEGG as a glycome informatics resource.
Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, Kawasaki T, Kanehisa M.

Marvin 16.5.2.0 – Draw & Visualize Chemistry

Marvin 16.5.2.0

:: DESCRIPTION

Marvin is a collection of tools for drawing, displaying and characterizing chemical structures, substructures and reactions.

::DEVELOPER

ChemAxon Ltd.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Marvin

:: MORE INFORMATION

ACD/ChemSketch 2015 – Draw Chemical Structures

ACD/ChemSketch 2015

:: DESCRIPTION

ACD/ChemSketch is a chemically intelligent drawing interface that allows you to draw almost any chemical structure including organics, organometallics, polymers, and Markush structures. It also includes features such as calculation of molecular properties (e.g., molecular weight, density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures (fewer than 50 atoms and 3 rings), and prediction of logP.Use it to produce professional looking structures and diagrams for reports and publications.

::DEVELOPER

Advanced Chemistry Development

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

ACD/ChemSketch

:: MORE INFORMATION

ArkMAP 2.78 – Draw and Align Genetic Maps

ArkMAP 2.78

:: DESCRIPTION

ArkMAP is a desktop application that allows users to draw and align genetic maps.

::DEVELOPER

Roslin Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Java

:: DOWNLOAD

 ArkMAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 13;14:246. doi: 10.1186/1471-2105-14-246.
ArkMAP: integrating genomic maps across species and data sources.
Paterson T, Law A.

PLT 7.1.19 – Draw Chemical Structures

PLT 7.1.19

:: DESCRIPTION

PLT is a program for producing chemical drawings and outputting them in a variety of formats. It will run on all versions of Windows (95, 98, NT, ME, 2000, XP, Vista, Win 7). PLT provides routines for producing all rings and line types used in chemical structures, formatted text material in any TrueType font installed on your system (including greek characters and special chemical characters like radical anion, radical cation, double dagger) and supports the use of color.

::DEVELOPER

Hans J. Reich

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PLT

:: MORE INFORMATION

MMDrawer 0.2.0.0 – Draw Chromosome Maps from the output of MapMaker EXP

MMDrawer 0.2.0.0

:: DESCRIPTION

MMDrawer is a simple program developed to draw chromosome maps from the output of MapMaker EXP.

::DEVELOPER

Emboss

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MMDrawer

:: MORE INFORMATION

loopDloop 2.07b – Draw RNA Secondary Structures

loopDloop 2.07b

:: DESCRIPTION

loopDloop is a tool for drawing RNA secondary structures in molecular biology. It will read files that include biosequence data with base pairing information.  It will display graphical views of the sequences secondary molecular structure.  Various options allow one to modify,adorn and edit the structure.   Standard application functions to save,print, edit and manage preferences are included.  This program will not estimate nor produce the base pairings needed for secondary structure. For that, other software such as RNAFOLD, MulFOLD, and multiple sequencealignment editors may be used.

::DEVELOPER

Don Gilbert at Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

loopDloop

:: MORE INFORMATION

Citaiton

Gilbert, D.G., 1996. loopDloop in Java, a Java application for visualizing RNA secondary structure. ftp://iubio.bio.indiana.edu/molbio/loopdloop/java/.