Raster3D 3.0-7 – Generate High Quality Raster Images of Proteins or other Molecules

Raster3D 3.0-7

:: DESCRIPTION

Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.

::DEVELOPER

Raster3D Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

MacOsx/Linux/Windows

:: DOWNLOAD

Raster3D

:: MORE INFORMATION

Citation

Merritt, Ethan A. and Bacon, David J. (1997).
“Raster3D: Photorealistic Molecular Graphics”
Methods in Enzymology 277, 505-524.

SliderII 1.1 – High Quality SNP Calling Using Illumina Data at Shallow Coverage

SliderII 1.1

:: DESCRIPTION

SliderII Results of SNPs concordance comparison to Maq.We used 68 lanes human whole genome shotgun sequencing, WGSS, PET data (real data), a total of 906 million reads sizes from 36 to 42 bases, using each of SliderII and MAQ, we aligned these reads to the human genome hg18 resulting a coverage of about 7.5 X. For each aligner, SNPs are sorted in descending order, using SNPs score for SliderII, and the Phred-like consensus quality score for MAQ. Concordance with Ensembl Variation 50 SNPs is used to compare SNPs calling accuracy.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX

:: DOWNLOAD

SliderII

:: MORE INFORMATION

Citation

Malhis et. al. 2008
High Quality Alignment and SNP Calling for Illumina High Throughput Sequence Data
Bioinformatics (2009) 25 (1): 6-13

HiFiX 1.0.6 – High-quality Sequence Clustering

HiFiX 1.0.6

:: DESCRIPTION

The software package HiFiX implements the novel algorithm for HIgh FIdelity Clustering of Sequences.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Mac / Linux
Python
BioPython

:: DOWNLOAD

HiFiX

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Apr 15;28(8):1078-85. doi: 10.1093/bioinformatics/bts098.
High-quality sequence clustering guided by network topology and multiple alignment likelihood.
Miele V, Penel S, Daubin V, Picard F, Kahn D, Duret L.

OGdraw 1.3.1 – Generate high-quality Graphical Maps of circular DNA Sequences

OGdraw 1.3.1

:: DESCRIPTION

OGDraw (OrganelleGenomeDraw) is a tool that enables the user to quickly generate high-quality graphical maps of circular DNA sequences. Though especially designed and optimized for the display of small organelle genomes like the chloroplast or mitochondrial genome, it is applicable to all circular DNA sequences. The input data can be provided as GenBank files or GenBank accession numbers.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX/Windows
Perl

:: DOWNLOAD

OGdraw

:: MORE INFORMATION

Citation
Nucleic Acids Res, 47 (W1), W59-W64 2019 Jul 2
OrganellarGenomeDRAW (OGDRAW) Version 1.3.1: Expanded Toolkit for the Graphical Visualization of Organellar Genomes
Stephan Greiner , Pascal Lehwark , Ralph Bock

Curr Genet. 2007 Nov;52(5-6):267-74. Epub 2007 Oct 24.
OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes.
Lohse M, Drechsel O, Bock R.