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