Bioinformatics ReviewBioinformatics Review
Notification Show More
Font ResizerAa
  •  Home
  • Docking
  • MD Simulation
  • Tools
  • More Topics
    • Softwares
    • Sequence Analysis
    • Algorithms
    • Bioinformatics Programming
    • Bioinformatics Research Updates
    • Drug Discovery
    • Phylogenetics
    • Structural Bioinformatics
    • Editorials
    • Tips & Tricks
    • Bioinformatics News
    • Featured
    • Genomics
    • Bioinformatics Infographics
  • Community
    • BiR-Research Group
    • Community Q&A
    • Ask a question
    • Join Telegram Channel
    • Join Facebook Group
    • Join Reddit Group
    • Subscription Options
    • Become a Patron
    • Write for us
  • About Us
    • About BiR
    • BiR Scope
    • The Team
    • Guidelines for Research Collaboration
    • Feedback
    • Contact Us
    • Recent @ BiR
  • Subscription
  • Account
    • Visit Dashboard
    • Login
Font ResizerAa
Bioinformatics ReviewBioinformatics Review
Search
Have an existing account? Sign In
Follow US
Sequence AnalysisSoftwareTools

Installing BLAT- A Pairwise Alignment Tool on Ubuntu

Tariq Abdullah
Last updated: August 25, 2020 3:24 pm
Tariq Abdullah
Share
1 Min Read
Installing BLAT on Ubuntu
SHARE

BLAT is a pairwise sequence alignment algorithm that is used in the assembly and annotation of the human genome [1]. In this article, we will install BLAT on Ubuntu.

Contents
Getting startedInstallationReference

Getting started

Let’s update and upgrade the system first.

$ sudo apt-get update

$ sudo apt-get upgrade

Installation

The first step in installing BLAT is to get libpng. Change to the directory where you want to install. In a terminal, type:

$ cd Downloads/

$ wget http://downloads.sourceforge.net/project/libpng/libpng16/older-releases/1.6.2/libpng-1.6.2.tar.gz

$ tar xvzf libpng-1.6.2.tar.gz

$ cd libpng-1.6.2/

$ ./configure --prefix=`pwd`

$ make

$ sudo make install

$ LIBPNGDIR=`pwd`

$ cd ../

Now, download and install BLAT.

$ wget http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip

$ unzip blatSrc35.zip

$ cd blatSrc/

$ cp $LIBPNGDIR/png.h lib/

$ cp $LIBPNGDIR/pngconf.h lib/

$ cp $LIBPNGDIR/pnglibconf.h lib/

$ echo $MACHTYPE

It will display the OS and hardware. For example, ‘x86_64-ubuntu-linux-gnu’.

$ MACHTYPE=x86_64

$ export MACHTYPE

$ mkdir -p ~/bin/$MACHTYPE

$ make

Export the path as shown below.

$ echo 'export MACHTYPE=x86_64' >> ~/.bashrc

$ echo 'export PATH=$PATH:~/bin/$MACHTYPE' >> ~/.bashrc

$ source ~/.bashrc

Now, you can easily run BLAT from the terminal. Type blatto run.


Reference

  1. Kent, W. J. (2002). BLAT—the BLAST-like alignment tool. Genome research, 12(4), 656-664.

TAGGED:BLATinstallationubuntu
Share This Article
Facebook Copy Link Print
ByTariq Abdullah
Tariq is founder of Bioinformatics Review and Lead Developer 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.
Leave a Comment

Leave a Reply Cancel reply

You must be logged in to post a comment.

- Advertisement -
Ad image
10 years of Bioinformatics Review: From a Blog to a Bioinformatics Knowledge Hub!
Editorial
Starting in Bioinformatics? Do This First!
Starting in Bioinformatics? Do This First!
Tips & Tricks
[Editorial] Is it ethical to change the order of authors’ names in a manuscript?
Editorial Opinion
Installing bbtools on Ubuntu
[Tutorial] Installing BBTools on Ubuntu (Linux).
Sequence Analysis Software Tools

You Might Also Like

DockingDrug DiscoverySoftwareTools

Beginner’s Guide for Docking using Autodock Vina

May 20, 2020
python scripts
DockingDrug DiscoverySoftwareTools

Prepare receptor and ligand files for docking using Python scripts

June 2, 2021
Generating multiple low-energy conformers using Avogadro
SoftwareTools

Generating multiple low-energy conformers using Avogadro

October 1, 2021
GenomicsSoftware

GenVisR : A tool for genomic visualization

May 20, 2020
Copyright 2024 IQL Technologies
  • Journal
  • Customer Support
  • Contact Us
  • FAQs
  • Terms of Use
  • Privacy Policy
  • Cookie Policy
  • Sitemap
Welcome Back!

Sign in to your account

Username or Email Address
Password

Lost your password?

Not a member? Sign Up