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Most widely used tools to analyze multiple sequence alignments

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Multiple sequence alignments (MSAs) are quite valuable in terms of studying new enzymes or organisms. They provide insights to identify their structures and functions. For this purpose, we need sophisticated tools to analyze large MSAs. This article will mention a few important and useful alignment viewers with various functions to perform on the MSAs.

1. Jalview

Jalview is another program to edit, modify, and visualize MSAs [1]. It offers a wide range of functions including analysis using phylogenetic trees, principal component analysis (PCA) plots, and molecular structure and annotation. You can easily import MSAs and group them using different colors and borders, name these groups. Besides, all the sequences can be sorted according to the associated phylogenetic tree. Additionally, the associated protein structure can also be analyzed simultaneously and export the alignment in different formats including the images. Creating sequence features is quite easy and these features can be exported for later use. It can be easily accessed on Windows/Linux/Mac using the web installer. The Linux package of Jalview can be easily used in a pipeline for sequence annotation and visualization and that’s why this is my favorite one. But the only limitation is that it requires more space and therefore, sometimes, it troubles in getting started which can be managed by allocating more memory to it.

2. Genedoc

Genedoc [2] is quite similar to Jalview and offers various features. It also offers to group sequences into different families/classes and export good quality images of MSAs. Motifs can be searched easily and the sequences can be annotated based on different properties such as physicochemical, sequence identities, hydrophobicity, conserved residues, and so on. It can be easily accessed on Windows but not yet available for Linux/Mac.

3. BioEdit

BioEdit is an intuitive multiple document interface having various features to modify alignments as per the requirements [3]. It is accessible on Windows 95/98/NT/2000/XP. It has several features including editing sequences, different modes of manual alignment, information-based alignment shading, the grouping and sorting of sequences, append alignments, capable of importing multiple formats such as .aln, .phy, and .fasta. Users can view and manipulate up to 20,000 sequences altogether. Other features include RNA comparative analysis, matrix plotter, phylogenetic tree viewer, and many more.

4. Unipro UGENE

It is a unified bioinformatics toolkit that offers many functions besides editing and visualizing MSAs [4]. It is available for Windows/Linux/Mac. The other key features of Unigene include fast sequence search, in-silico PCR, NCBI, Genbank BLAST search, ORF finder, restriction enzyme finder, genome mapping, raw NGS data processing, visualization of BAM files, protein structure viewer, mRNA alignment, and so on.

5. AliView

AliView is another alignment viewer and editor for MSAs but it is fast to operate [5]. It also offers several functions such as sequence sorting by name and residues, moving sequences, codon positions, find primers in the conserved regions, alignment using MUSCLE or MAFFT. It imports various formats such as .fasta, .msf, .nexus, and .phy and exports alignment as an image (PNG). It is available for Windows/Linux/Mac.

There are several other alignment visualizers, these are the most commonly used ones and offer a wide range of features.

References

  1. Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009) “Jalview Version 2 – a multiple sequence alignment editor and analysis workbench” Bioinformatics25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
  2. Nicholas, K. B. (1997). GeneDoc: analysis and visualization of genetic variation. Embnew. news4, 14.
  3. Hall, T. A. (1999, January). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In Nucleic acids symposium series (Vol. 41, No. 41, pp. 95-98). [London]: Information Retrieval Ltd., c1979-c2000.
  4. Okonechnikov, K., Golosova, O., Fursov, M., & Ugene Team. (2012). Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics28(8), 1166-1167.
  5. Larsson, A. (2014). AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics30(22), 3276-3278.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

Bioinformatics Programming

Free_Energy_Landscape-MD: Python package to create Free Energy Landscape using PCA from GROMACS.

Dr. Muniba Faiza

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In molecular dynamics (MD) simulations, a free energy landscape (FEL) serves as a crucial tool for understanding the behavior of molecules and biomolecules over time. It is difficult to understand and plot a meaningful FEL and then extract the time frames at which the plot shows minima. In this article, we introduce a new Python package (Free_Energy_Landscape-MD) to generate an FEL based on principal component analysis (PCA) from MD simulation done by GROMACS [1].

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Bioinformatics News

VS_Analysis: A Python package to perform post-virtual screening analysis

Dr. Muniba Faiza

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VS_Analysis: A Python package to perform post-virtual screening analysis

Virtual screening (VS) is a crucial aspect of bioinformatics. As you may already know, there are various tools available for this purpose, including both paid and freely accessible options such as Autodock Vina. Conducting virtual screening with Autodock Vina requires less effort than analyzing its results. However, the analysis process can be challenging due to the large number of output files generated. To address this, we offer a comprehensive Python package designed to automate the analysis of virtual screening results.

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Bioinformatics Programming

vs_interaction_analysis.py: Python script to perform post-virtual screening analysis

Dr. Muniba Faiza

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vs_interaction_analysis.py: Python script to perform post-virtual screening analysis

Analyzing the results of virtual screening (VS) performed with Autodock Vina [1] can be challenging when done manually. In earlier instances, we supplied two scripts, namely vs_analysis.py [2,3] and vs_analysis_compounds.py [4]. This time, we have developed a new Python script to simplify the analysis of VS results.

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Software

How to install Interactive Genome Viewer (IGV) & tools on Ubuntu?

Dr. Muniba Faiza

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How to install Interactive Genome Viewer (IGV) & tools on Ubuntu?

Interactive Genome Viewer (IGV) is an interactive tool to visualize genomic data [1]. In this article, we are installing IGV and tools on Ubuntu desktop.

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MD Simulation

[Tutorial] Installing VIAMD on Ubuntu (Linux).

Dr. Muniba Faiza

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[Tutorial] Installing VIAMD on Ubuntu (Linux).

Visual Interactive Analysis of Molecular Dynamics (VIAMD) is a tool that allows the interactive analysis of molecular dynamics simulations [1]. In this article, we are installing it on Ubuntu (Linux).

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Docking

[Tutorial] Performing docking using DockingPie plugin in PyMOL.

Dr. Muniba Faiza

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[Tutorial] Performing docking using DockingPie plugin in PyMOL.

DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.

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Docking

How to install the DockingPie plugin on PyMOL?

Dr. Muniba Faiza

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How to install DockingPie plugin on PyMOL?

DockingPie [1] is a plugin of PyMOL [2] made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).

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Software

Video Tutorial: Calculating binding pocket volume using PyVol plugin.

Dr. Muniba Faiza

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Calculate Binding Pocket Volume in Pymol (using PyVol plugin).

This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].

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Software

How to generate topology from SMILES for MD Simulation?

Dr. Muniba Faiza

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How to generate topology from SMILES for MD Simulation?

If you need to generate the topology of molecules using their SMILES, a simple Python script is available.

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Software

[Tutorial] Installing jdock on Ubuntu (Linux).

Dr. Muniba Faiza

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[Tutorial] Installing jdock on Ubuntu (Linux).

jdock is an extended version of idock [1]. It has the same features as the idock along with some bug fixes. However, the binary name and the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).

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Software

How to upgrade cmake on Ubuntu (Linux)?

Dr. Muniba Faiza

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How to upgrade cmake on Ubuntu/Linux?

In bioinformatics, cmake is used to install multiple software including GROMACS, jdock, and so on. Here is a short tutorial on how to upgrade cmake on Ubuntu and get rid of the previous version. (more…)

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Software

How to install GMXPBSA on Ubuntu (Linux)?

Dr. Muniba Faiza

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How to install GMXPBSA on Ubuntu (Linux)?

GMXPBSA is a tool to calculate binding free energy [1]. It is compatible with Gromacs version 4.5 and later. In this article, we will install GMXPBSA version 2.1.2 on Ubuntu (Linux).

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Docking

[Tutorial] Installing Pyrx on Windows.

Dr. Muniba Faiza

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[Tutorial] Installing Pyrx on Windows.

Pyrx [1] is another virtual screening software that also offers to perform docking using Autodock Vina. In this article, we will install Pyrx on Windows. (more…)

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MD Simulation

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Dr. Muniba Faiza

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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.

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Software

Installing Autodock4 on MacOS.

Dr. Muniba Faiza

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Installing Autodock4 on MacOS

Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.

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Docking

How to install Autodock4 on Ubuntu?

Dr. Muniba Faiza

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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.

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Software

DS Visualizer: Uses & Applications

Dr. Muniba Faiza

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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.

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Software

Protein structure & folding information exploited from remote homologs.

Dr. Muniba Faiza

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protein structure & folding prediction using 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…)

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RNA-seq analysis

Pathonoia- A new tool to detect pathogens in RNA-seq data.

Dr. Muniba Faiza

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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].

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Software

AlphaFill- New algorithm to fill ligands in AlphaFold models.

Dr. Muniba Faiza

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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…)

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