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.
Let’s update and upgrade the system first.
Open the terminal (Ctrl+T) and type the following commands:
$ sudo apt-get update
$ sudo apt-get upgrade
Change to the directory where you wish to download the software.
$ cd Downloads/
Make a new directory named “fastx-toolkit” where we will install the binaries.
$ mkdir fastx_toolkit
Move inside this directory and download the toolkit. You can either download it from here or use the following command:
$ cd fastx_toolkit/
$ wget http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
Now extract the downloaded archive file using the following commands:
$ tar xvf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
You will be able to see the binaries. Now, add these binaries to your path.
$ sudo cp ./bin/* /usr/local/bin
Now, you can easily use all the binaries from the terminal by entering their names.
- Gordon, A., & Hannon, G. J. (2010). Fastx-toolkit. FASTQ/A short-reads preprocessing tools (unpublished) http://hannonlab. cshl. edu/fastx_toolkit, 5.
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…)
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NGlyAlign- A New Tool to Align Highly Variable Regions in HIV Sequences
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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…)
Aligning DNA reads against a local database using DIAMOND
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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…)
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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…)
A short introduction to protein structures modification and ModFinder
A lot of protein structures are determined on a large scale and submitted in Protein Data Bank (PDB) www.rcsb.org . After the experimental determination of these structures, they are used in many scientific studies and experiments are performed upon them such as mutagenesis, docking, and so on. (more…)