Software
Alvis- A New Tool for Alignment & Visualization of Contigs & Reads and Chimera Detection
Visualization of running alignments of reads and contigs facilitates easy analysis and is useful in presenting assembly results. Several tools such as Artemis, BLAST Web, Circos, and so on, exist. A new tool called Alvis is developed for easy alignment and visualization of contigs and reads [1]. It can also be used for chimera detection.
Alvis is a user-friendly command-line tool capable of generating visuals of common alignment tasks. It can generate four different kinds of diagrams and accepts the input in different formats including BLAST tabular, PAF format from minimap2, SAM files, PSL file, and MUMmer’s .coords and .tiling files. Users can also filter the alignments. Alvis highlights the potential chimeric contigs or reads in the output.
The visualization output of Alvis includes:
- alignment diagram,
- contig alignment diagram,
- coverage map diagram, and
- genome coverage diagram.
Alvis is written in Java with a simple command-line interface. It is platform-independent unless it consists of a Java Runtime Environment. Alvis is freely downloadable from Github.
For more information, read here.
References
- Martin, S., Leggett, R.M. (2021). Alvis: a tool for contig and read ALignment VISualisation and chimera detection. BMC Bioinformatics 22, 124.
MD Simulation
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.
Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.
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.
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.
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…)
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].
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…)
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.
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…)
While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.
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…)
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…)
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…)
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…)
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…)
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…)
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.
Previously, we provided a tutorial for Pymol installation on Ubuntu. In this article, we are going to install Pymol on Mac OS. (more…)
In this article, we are going to install VMD [1] on Ubuntu. (more…)
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