GrammR 1.1.0 – Graphical Representation and Modeling of Metagenomic reads

GrammR 1.1.0

:: DESCRIPTION

GrammR represents metagenomic samples on the Euclidean space to examine similarity amongst samples by studying clusters in the model. Given the matrix of metagenomic counts for samples, this package (1) quantifies dissimilarity between samples using Kendall’s tau-distance, (2) constructs multidimensional models of different dimension, and (3) plots the models for visualization and comparison.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOs
  • R

:: DOWNLOAD

 GrammR

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jan 20. pii: btv032. [Epub ahead of print]
GrammR: Graphical Representation and Modeling of Count Data with Application in Metagenomics.
Ayyala DN, Lin S

JOY 5.0 – Protein Sequence-Structure Representation and Analysis

JOY 5.0

:: DESCRIPTION

JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and help understand the conservation of amino acids in their specific local environments. For instance, it has been recognised that a sidechain hydrogen-bonded to a main-chain amide plays an important role in stabilizing the 3D structure and is generally well conserved during evolution. Such a residue is shown in a bold-face letter in the formatted alignments. Another example is the importance of solvent inaccessible residues which are shown in UPPER-CASE letters.

::DEVELOPER

the Mizuguchi Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 JOY

:: MORE INFORMATION

Citation

Mizuguchi, K., Deane, C.M., Blundell, T.L., Johnson,M.S. and Overington, J.P. (1998)
JOY: protein sequence-structure representation and analysis.
Bioinformatics 14:617-623.

2D-MH – Generating Graphic Representation of Protein Sequences

2D-MH

:: DESCRIPTION

2D-MH is a web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids.

::DEVELOPER

JCI BioInfo Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

2D-MH: A web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids.
Wu ZC, Xiao X, Chou KC.
J Theor Biol. 2010 Nov 7;267(1):29-34. doi: 10.1016/j.jtbi.2010.08.007.

LORS – LOw-Rank Representation and Sparse Regression for eQTL mapping

LORS

:: DESCRIPTION

LORS is a LOw-Rank representation and Sparse regression for eQTL mapping. This algorithm accounts for confounding factors such as unobserved covariates, experimental artifacts, and unknown environmental perturbations

::DEVELOPER

Hongyu Zhao’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/MacOsX
  • MatLab

:: DOWNLOAD

 LORS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 17.
Accounting for Non-Genetic Factors by Low-Rank Representation and Sparse Regression for eQTL Mapping.
Yang C, Wang L, Zhang S, Zhao H.

Grammar String – novel ncRNA Secondary Structure Representation

Grammar String

:: DESCRIPTION

Grammar String is a novel representation of noncoding RNA secondary structure. By encoding both the sequence and secondary structure of ncRNAs in a string, ncRNA structural alignment is converted to sequence alignment. The software package provides an ncRNA consensus secondary structure derivation tool.

There are three sub-programs
1. ct2ss: The program to convert .ct file to secondary structure
2. ss2gs: The program to generate grammar string from sequence and structure
3. msa: The alignment program, pair-wise and multiple alignment program

::DEVELOPER

Yanni Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Grammar String

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2011 Apr;9(2):317-37.
ncRNA consensus secondary structure derivation using grammar strings.
Achawanantakun R, Sun Y, Takyar SS.

CellPublisher 2.0 – Representations of Biochemical Processes

CellPublisher 2.0

:: DESCRIPTION

CellPublisher is a free and open program to make highly interactive representations of biochemical processes. It converts a file created in the popular modelling tool CellDesigner into a Google maps-based version inside a browser.

::DEVELOPER

Lope A. Flórez, Christoph R. Lammers, Raphael Michna and Jörg Stülke, Department of General Microbiology, Georg-August University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 CellPublisher

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Dec 1;26(23):2997-9. Epub 2010 Oct 14.
CellPublisher: a web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways.
Flórez LA, Lammers CR, Michna R, Stülke J.

GSE – Database System for the Representation, Retrieval, and Analysis of Microarray data

GSE

:: DESCRIPTION

GSE (Genomic Spatial Events system) is a database for storing, visualizing, and analyzing ChIP-based transcription factor binding data and gene expression data.

::DEVELOPER

the Gifford Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GSE

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2008:539-50.
GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data.
Danford T, Rolfe A, Gifford D.