In continuation with the series under “Do you Hyphy…”, this article envisages another very important analytical tool that Datamonkey web server provides us called EVOBLAST[1,2]. EVOBALST stands for Evolutionary Fingerprinting Analysis Results. It is a remarkable tool which identifies a. whether a multiple sequence alignment datasets (in partitions or globally) is under different rates of evolution i.e. different dN/dS rates over different regions/partitions, signifying positive or negative selection (for details read previous articles on this series), b. and if they are found to be evolving differentially, then it also depicts in a graphical form which regions in the multiple sequence alignment are under positive, negative or neutral selection.
To run this module, gene coding sequence dataset is required to be uploaded on data analysis page. Select a suitable substitution model (one can use the Model Select module for this, also available on the Datamonkey web server) and select Evolutionary Fingerprinting option, based on 1000 distribution samples from the drop-down menu. Depending on the size of the query dataset, the remote computer cluster will take few minutes to several minutes and will return with Maximum Likelihood Estimates (MLE) as well as the graph (such as the one shown in Figure 1) depicting the estimate of the distribution of synonymous and non-synonymous rates inferred from the alignments. The pink pixels and the intensity of the pink shade (light pink to dark pink) for each pixel show the maximum likelihood estimate/probability of the selection pressure of a site/region undergoing negative, positive or neutral selection. The diagonal line shows the neutral evolution (mostly no change or non-synonymous changes). Thus regions falling on the diagonal line are under neutral evolution while the regions above the diagonal line are under non-synonymous or purifying or positive selection. Similarly, regions with pink pixels below the diagonal line are under negative selection. Although, the depiction and MLE are highly accurate and the graph output so obtained is of publication quality but still it is highly recommended that the finding of this module must be correlated with other similar data output based modules/application to strengthen the interpretation.
1. Delport, W., Poon, A.F., Frost, S.D.W., Kosakovsky Pond, S.L., 2010. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26(19): 2455–2457
2. Kosakovsky Pond, S.L., Frost, S.D.W., 2005. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21(10): 2531-2533
3. Kosakovsky Pond SL, et al., 2010. Evolutionary fingerprinting of genes. Molecular Biology and Evolution 27:520–536.
HMMER- Uses & Applications
Easy installation of some alignment software on Ubuntu (Linux) 18.04 & 20.04
There are commonly used alignment programs such as muscle, blast, clustalx, and so on, that can be easily installed from the repository. In this article, we are going to install such software on Ubuntu 18.04 & 20.04. (more…)
FEGS- A New Feature Extraction Model for Protein Sequence Analysis
Protein sequence analyses include protein similarity, Protein function prediction, protein interactions, and so on. A new feature extraction model is developed for easy analysis of protein sequences. (more…)
Installing RDPTools on Ubuntu (Linux)
RDP provides analysis tools called RDPTools. These tools are used to high-throughput sequencing data including single-strand, and paired-end reads . In this article, we are going to install RDPTools on Ubuntu (Linux). (more…)
NGlyAlign- A New Tool to Align Highly Variable Regions in HIV Sequences
It is necessary to detect highly variable regions in envelopes of viruses as it allows the establishment of the viruses in the human body. A new tool is developed to build and align the highly variable regions in HIV sequences. (more…)
How to install ClustalW2 on Ubuntu?
Clustal packages [1,2] are quite useful in multiple sequence alignments. Especially, when you need specific outputs from the command-line. In this article, we will install CustalW2 command-line tool on Ubuntu. (more…)
Installing HMMER package on Ubuntu
HMMER tool is used for searching sequence homologs using profile hidden Markov Models (HMMs) . It is also one of the most widely used alignment tools. In this article, we will install the latest HMMER package on Ubuntu. (more…)
Installing FASTX-toolkit on Ubuntu
FASTX-toolkit is a command-line bioinformatics software package for the preprocessing of short reads FASTQ/A files . These files contain multiple short-read sequences obtained as an output of next-generation sequencing. In this article, we are going to install FASTX-toolkit on Ubuntu. (more…)
Aligning DNA reads against a local database using DIAMOND
DIAMOND is a program for high throughput pairwise alignment of DNA reads and protein sequences . It is used for the high-performance analysis of large sequence data. In this article, we will make a local database of protein sequences and align protein sequences against the reference database. (more…)
Installing MEME suite on Ubuntu
Installing BLAT- A Pairwise Alignment Tool on Ubuntu
Homology search against a local dataset using NCBI-BLAST+ command-line tool
NCBI-BLAST+  command-line tool offers multiple functions to be performed on a large dataset of sequences. Previously, we have shown how to blast against a local dataset of sequences. This article will explain the search of homologous sequences for a query sequence against a local database of sequences and how to obtain the top 100 hits out of the searched results. (more…)
How to use Clustal Omega and MUSCLE command-line tools for multiple sequence alignment?
Clustal Omega [1,2] and MUSCLE are bioinformatics tools that are used for multiple sequence alignment (MSA). In one of our previous articles, we explained the usage of the ClustalW2 command-line tool for MSA and phylogenetic tree construction. In this article, we will use Clustal Omega and MUSCLE for MSA exploring other arguments that facilitate different output formats. (more…)
Multiple Sequence Alignment and Phylogenetic Tree construction using ClustalW2 command-line tool
ClustalW2 is a bioinformatics tool for multiple sequence alignment of DNA or protein sequences. It can easily align sequences and generate a phylogenetic tree online (https://www.genome.jp/tools-bin/clustalw). However, in some cases, we need to perform these operations on a large number of FASTA sequences using the command-line tool of ClustalW2 . (more…)
Sequence search against a set of local sequences (local database) using phmmer
PHMMER is a sequence analysis tool used for protein sequences (http://hmmer.org; version 3.1 b2). It is available online as a web server and as well as a part of the HMMER stand-alone package (http://hmmer.org; version 3.1 b2). HMMER offers various useful features such as multiple sequence alignment including the file format conversion. (more…)
Biotite: A bioinformatics framework for sequence and structure data analysis
Sequence and structural data in bioinformatics are ever-increasing and the need for its analysis is ever-demanding likewise. As bioinformaticians analyze the data with their keen knowledge and reach important conclusions, similarly, bioinformaticists provide with the enhanced and advanced tools and software for data analysis. (more…)
Simulated sequence alignment software: An alternative to MSA benchmarks
In our previous article, we discussed different multiple sequence alignment (MSA) benchmarks to compare and assess the available MSA programs. However, since the last decade, several sequence simulation software have been introduced and are gaining more interest. In this article, we will be discussing various sequence simulating software being used as alternatives to MSA benchmarks. (more…)
Benchmark databases for multiple sequence alignment: An overview
Multiple sequence alignment (MSA) is a very crucial step in most of the molecular analyses and evolutionary studies. Many MSA programs have been developed so far based on different approaches which attempt to provide optimal alignment with high accuracy. Basic algorithms employed to develop MSA programs include progressive algorithm , iterative-based , and consistency-based algorithm . Some of the programs incorporate several other methods into the process of creating an optimal alignment such as M-COFFEE  and PCMA . (more…)
The basic local alignment search tool (BLAST) [1,2] is known for its speed and results, which is also a primary step in sequence analysis. The ever-increasing demand for processing huge amount of genomic data has led to the development of new scalable and highly efficient computational tools/algorithms. For example, MapReduce is the most widely accepted framework which supports design patterns representing general reusable solutions to some problems including biological assembly  and is highly efficient to handle large datasets running over hundreds to thousands of processing nodes . But the implementation frameworks of MapReduce (such as Hadoop) limits its capability to process smaller data. (more…)
Role of Information Theory, Chaos Theory, and Linear Algebra and Statistics in the development of alignment-free sequence analysis
Sequence alignment is customary to not only find similar regions among a pair of sequences but also to study the structural, functional and evolutionary relationship between organisms. Many tools have been discovered to achieve the goal of alignment of a pair of sequences, separately for nucleotide sequence and amino acid sequence, BLOSSUM & PAM  are a few to name. (more…)