MUSCLE v/s T-COFFEE : An overview and different aspects
As I have discussed in my earlier articles about the multiple sequence alignment (MSA) tools (MUSCLE & T-COFFEE). Now in this article, we will discuss different aspects of these tools and which one is more preferred over the another. MUSCLE and T-COFFEE both are multiple sequence alignment tools and also helps to study the evolutionary relationships among the species.As I have already explained the algorithms involved in both the tools which are comparable. During the alignment using MUSCLE, it uses the UPGMA tree construction method which assumes that mutation occurs at the constant rate. This may be a fact which makes it different from other tools.
On the positive side, MUSCLE is a tool which is known for its speed and accuracy on each of the four benchmark test sets ( BAliBASE, SABmark, SMART and PREFAB). It is much faster than other MSA tools. MUSCLE also uses a progressive alignment which is iterated while it gets a better SP score (explained in “Basic concept of MSA” article).
T-COFFEE is an improvisation over MUSCLE in the sense that it combines both global and local alignments which provides better results and it also qualifies the four benchmark tests. Second thing which makes it better than other tools is that it uses an optimization method which provides the multiple alignment that best fits in the input library. T-COFFEE also uses progressive alignment strategy similar to MUSCLE, but unlike MUSCLE, T-COFFEE uses Neighbor Joining tree construction method during alignment which corrects the assumption of UPGMA method and assumes that mutation never occurs at a constant rate.
Let us take protein sequences of ‘Keratin’ protein of few species and align them using both the tools and construct the respective phylogeny trees. In this example, I have taken FASTA sequences of: Homo sapiens (GI: 7717238) , Paralichthys olivaceus (GI: 10716084), Pseudomonas viridiflava (GI: 934022154) and Pseudomonas aeruginosa (GI: 856785229). The results are as follows:
Fig 1. Tree constructed using MUSCLE.
Fig 2. Tree constructed using T-COFFEE.
As we have seen both the trees are slight different. The sequence of Paralichthys olivaceus is placed below to that of Homo sapiens, but it is placed above in tree constructed by T-COFFEE. Similarly, this is case with other two species. This is how MUSCLE & T-COFFEE are different from each other. T-COFFEE is more preferred over MUSCLE while aligning both closely or distantly related species but MUSCLE ia more suitable to align distantly related species since it uses global alignment only, but T-COFFEE uses both.
An exhaustive list of references for this article is available with the author and is available on personal request, for more details write to [email protected]
DS Visualizer: Uses & Applications
Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins . Here are some uses and applications of DS Visualizer.
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…)
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 .
AlphaFill- New algorithm to fill ligands in AlphaFold models.
AlphaFold is a popular artificial intelligence based protein prediction tool . 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.,. (more…)
How to calculate binding pocket volume using PyVol plugin in PyMol?
Previously, we provided a tutorial for PyVol plugin  installation. In this article, we will calculate the binding pocket volume of protein using the same plugin in PyMol . (more…)
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.
Installing PyVOL plugin in Pymol on Ubuntu (Linux).
PyVOL  is an excellent plugin of Pymol  for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)
How to execute matlab from terminal in Ubuntu (Linux)?
While trying to install Matlab , it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.
How to install Kpax on Ubuntu (Linux)?
Kpax is a bioinformatics program to search and align protein structures . 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…)
How to run do_dssp command (mkdssp) in Gromacs 2022?
In the latest version of GROMACS (2022) , 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…)
Installing SMINA on Ubuntu (Linux).
SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy minimization . In this article, we are going to install SMINA on Ubuntu (Linux). (more…)
How to install ClusCo on Ubuntu (Linux)?
ClusCo is a bioinformatics software to perform clustering and comparison of protein models . In this article, we are going to install ClusCo on Ubuntu (Linux). (more…)
How to run LigAlign plugin on Pymol?
Running a plugin on an old version of Pymol  can give you multiple errors that are not easy to troubleshoot. For example, LigAlign plugin  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…)
How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?
Few errors appear when we try to run the LigAlign plugin  in Pymol . 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…)
How to install multiple Pymol versions on Ubuntu (Linux)?
Sometimes we need to access old versions of Pymol . 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.
[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…)
How to install VMD on Ubuntu?
In this article, we are going to install VMD  on Ubuntu. (more…)
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  on Mac OS. (more…)
PyMol: Uses & Applications
PyMol is one of the most widely used bioinformatics software. Generally, it is used as a molecular viewer to visualize macromolecules and small molecules. In this article, we are discussing several uses and applications of PyMol. (more…)
How to take snapshots of structure at specific times in GROMACS?
It is important to see the behavior of protein during an MD simulation. This can be achieved by taking snapshots in the form of PDB format. In this article, we have provided a few commands that you can use to take snapshots of a complete system or protein during MD simulation. (more…)
You must be logged in to post a comment Login