Software
GIANT: A New Tool for Transcriptomic Data Analysis

Transcriptomic data analysis is an important requirement in biomedical research. The bioinformatics tools available for transcriptomic data analysis provide a user-friendly interface that is easily accessible by the experimental biologists as well. A new tool called GIANT-Galaxy-based tool for Interactive ANalysis of Transcriptomic data has been developed by Vandel et al., [1].
GIANT is a set of tools allowing researchers to analyze transcriptomic data from microarray or RNA-seq analyses [1]. It consists of different modules facilitating the easy selection of tools for a particular analysis. The source code of the GIANT is freely downloadable on Github (https://github.com/juliechevalier/GIANT). The Galaxy tool suite is available on the Galaxy Main Tool Shed (https://toolshed.g2.bx.psu.edu; name:suite_giant; owner:vandelj).
How GIANT works?
GIANT takes raw data from microarray or RNA-seq. Depending upon that, it selects methodology to process the data.
- Firstly, it subjects the input data to a quality check.
- In the next step, it leads to normalization including differential analysis in both the cases (microarray and RNA-seq).
- After differential analysis, the data is subjected to another quality check. It is highly recommended [1].
- After that, it generates volcano plots and heatmaps, performs clustering and GSEA formatting as per the user requirements.
GIANT suite consists of various adjustable parameters to improve the analysis and visualization of transcriptomic data. As an output, it provides interactive plots, tabular results, and easy visualization and sharing of the data. For further reading, click here.
References
- Vandel, J., Gheeraert, C., Staels, B., Eeckhoute, J., Lefebvre, P., & Dubois-Chevalier, J. (2020). GIANT: Galaxy-based tool for Interactive ANalysis of Transcriptomic data. Scientific Reports.
Docking
How to install Autodock4 on Ubuntu?

Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.
Software
DS Visualizer: Uses & Applications

Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins [1]. Here are some uses and applications of DS Visualizer.
Software
Protein structure & folding information exploited from remote homologs.

Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)
RNA-seq analysis
Pathonoia- A new tool to detect pathogens in RNA-seq data.

Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].
Software
AlphaFill- New algorithm to fill ligands in AlphaFold models.

AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)
Software
How to calculate binding pocket volume using PyVol plugin in PyMol?
Software
How to generate electron density map using Pymol?

Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.
Software
Installing PyVOL plugin in Pymol on Ubuntu (Linux).

PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)
Software
How to execute matlab from terminal in Ubuntu (Linux)?

While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.
Software
How to install Kpax on Ubuntu (Linux)?

Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)
Secondary structure
How to run do_dssp command (mkdssp) in Gromacs 2022?

In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)
Software
Installing SMINA on Ubuntu (Linux).

SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy minimization [1]. In this article, we are going to install SMINA on Ubuntu (Linux). (more…)
Software
How to install ClusCo on Ubuntu (Linux)?

ClusCo is a bioinformatics software to perform clustering and comparison of protein models [1]. In this article, we are going to install ClusCo on Ubuntu (Linux). (more…)
Software
How to run LigAlign plugin on Pymol?

Running a plugin on an old version of Pymol [1] can give you multiple errors that are not easy to troubleshoot. For example, LigAlign plugin [2] runs on an old version of Pymol. Previously, we explained how to install LigAlign on Pymol. In this article, we will run the LigAlign command on Pymol. (more…)
Software
How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?

Few errors appear when we try to run the LigAlign plugin [1] in Pymol [2]. For example, if you try to run the ligand_alignment plugin, it will give you multiple errors including “Unable to initialize LigAlign v1.00“, or “can’t run LigAlign v1.00” or “incorrect Python syntax” or “Plugin has been installed but initialization failed“. In this article, we explain the reason for this issue and how you can rectify these errors. (more…)
Software
How to install multiple Pymol versions on Ubuntu (Linux)?

Sometimes we need to access old versions of Pymol [1]. Running some plugins on Pymol is difficult due to Python incompatibility. New Pymol versions require Python 3.x whereas older versions run on Python 2.x. Therefore, we need to maintain multiple versions of Pymol on a single system. In this article, we will install Pymol 1.7.x along with the latest version (Pymol 2.5.2) on Ubuntu. Later, we will create shortcuts for them.
Software
[Tutorial] Installing Pymol on Mac OS.

Previously, we provided a tutorial for Pymol installation on Ubuntu. In this article, we are going to install Pymol on Mac OS. (more…)
Software
How to install VMD on Ubuntu?

In this article, we are going to install VMD [1] on Ubuntu. (more…)
MD Simulation
How to install GROMACS on Apple M1 (MacOS)?

We have provided a few articles on GROMACS installation on Ubuntu. In this article, we are going to install GROMACS [1] on Mac OS. (more…)
You must be logged in to post a comment Login