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:
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].
[Tutorial] Performing docking using DockingPie plugin in PyMOL.
How to install the DockingPie plugin on PyMOL?
DockingPie  is a plugin of PyMOL  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).
Video Tutorial: Calculating binding pocket volume using PyVol plugin.
How to generate topology from SMILES for MD Simulation?
[Tutorial] Installing jdock on Ubuntu (Linux).
jdock is an extended version of idock . 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).
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…)
How to install GMXPBSA on Ubuntu (Linux)?
[Tutorial] Installing Pyrx on Windows.
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS  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.
Installing Autodock4 on MacOS.
How to install Autodock4 on Ubuntu?
DS Visualizer: Uses & Applications
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…)