BioGem.Org

Running Swiss-PdbViewer on Ubuntu

Ashok Kumar — Sat, 03 Jul 2010 07:44:08 +0000

DeepView – Swiss-PdbViewer (or SPDBV) is an bioinformatics application that provides a user friendly graphical interface allowing to view and analyze protein and nucleic acid structure. This program is associated with Swiss-Model (an automated homology modeling server running in the Geneva Glaxo Welcome Experimental Research), accessible via the ExPASy web server. Through this application, proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing.

Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modeling tools are integrated and command files for popular energy minimization packages can be generated.

Currently Swiss-PdbViewer is released for Microsoft Windows and Macintosh OS. In order to run Swiss-PdbViewer in Ubuntu OS, a windows application loader WINE must be installed.

What is Wine?

Wine is an implementation of Windows APIs on top of X and Unix. Think of Wine as a Windows compatibility layer. Wine provides a program loader, allowing many unmodified Windows binaries to run under Intel Unixes. Wine works on most popular Intel Unixes, including Linux, FreeBSD, and Solaris.

In Linux Ubuntu OS, Wine can be easily installed through Ubuntu Software Center.

Steps to install Wine

To install Wine, simply follow these steps.

1. Go to Applications -> Ubuntu Software Center.

2. Click the tab Get Free Software.
3. In the search bar type keyword “wine“.

4. Select the hit Wine Microsoft Windows Compatibility Layer and press forward button.
5. Click the Install button.

Steps to run SPDBV

1. Download the windows compatible Swiss-PdbViewer application from SPDBV download site and decompress it.
2. Open the decompressed folder. Right click the application spdbv.exe and open with Wine Windows Program Loader.

Other bioinformatics tools such as RasMol, Clustal X, TreeView, SeaView, PyMOL, Cn3D, EMBOSS, fastDNAml, etc can be installed instantly through Ubuntu Software Center.

Note: You must be on-line while installing the application.

Embedding Perl into Perl

Ashok Kumar — Sun, 06 Jun 2010 17:39:24 +0000

This article describes embedding a Perl script into a Perl script. This program is an Common Gateway Interface, which reads ASCII files through file upload and displays content of the file. The Perl script upload.pl is called through the Perl script file-upload.pl using function eval{ }. This program can be modified to call by reference function, to access in other programs too.

file-upload.html

File Upload

file-upload.pl
#!/usr/bin/perl
eval { require “upload.pl” };
my @x = upload();
print “Content-type: text/html\n\n”;
print “”,@x,””;

upload.pl
#!/usr/bin/perl
use strict ‘refs’;
use lib ‘..’;
use CGI qw(:standard);
use CGI::Carp qw(fatalsToBrowser);
sub upload()
{
my $file = param(’file’);
while ()
{
@_ = <$file>;
}
return (@_);
}

Note: Both Perl scripts must granted file permission (0755)

RNA to Protein Translation in PERL

Ashok Kumar — Tue, 09 Mar 2010 16:11:44 +0000

In PERL programing, RNA sequence is converted into protein sequence by substituting equivalent amino acid characters to triplet characters of RNA. This method is followed to find six reading frame (three in forward direction, and three in reverse direction). In this program, I have used associative array (also known as hash array) to associate triplet characters with amino acid character.

The associate array corresponding to codon table is arranged to 20 amino acid character. The triplet codon table is shown bellow:

Source Code:

print “Enter the RNA sequence: “;
$rna = <>;
chomp($rna);
$rna =~s/[^acgu]//ig;
my $rna = uc($rna);
my(%genetic_code) = (
‘UCA’ => ‘S’, # Serine
‘UCC’ => ‘S’, # Serine
‘UCG’ => ‘S’, # Serine
‘UCU’ => ‘S’, # Serine
‘UUC’ => ‘F’, # Phenylalanine
‘UUU’ => ‘F’, # Phenylalanine
‘UUA’ => ‘L’, # Leucine
‘UUG’ => ‘L’, # Leucine
‘UAC’ => ‘Y’, # Tyrosine
‘UAU’ => ‘Y’, # Tyrosine
‘UAA’ => ‘_’, # Stop
‘UAG’ => ‘_’, # Stop
‘UGC’ => ‘C’, # Cysteine
‘UGU’ => ‘C’, # Cysteine
‘UGA’ => ‘_’, # Stop
‘UGG’ => ‘W’, # Tryptophan
‘CUA’ => ‘L’, # Leucine
‘CUC’ => ‘L’, # Leucine
‘CUG’ => ‘L’, # Leucine
‘CUU’ => ‘L’, # Leucine
‘CCA’ => ‘P’, # Proline
‘CAU’ => ‘H’, # Histidine
‘CAA’ => ‘Q’, # Glutamine
‘CAG’ => ‘Q’, # Glutamine
‘CGA’ => ‘R’, # Arginine
‘CGC’ => ‘R’, # Arginine
‘CGG’ => ‘R’, # Arginine
‘CGU’ => ‘R’, # Arginine
‘AUA’ => ‘I’, # Isoleucine
‘AUC’ => ‘I’, # Isoleucine
‘AUU’ => ‘I’, # Isoleucine
‘AUG’ => ‘M’, # Methionine
‘ACA’ => ‘T’, # Threonine
‘ACC’ => ‘T’, # Threonine
‘ACG’ => ‘T’, # Threonine
‘ACU’ => ‘T’, # Threonine
‘AAC’ => ‘N’, # Asparagine
‘AAU’ => ‘N’, # Asparagine
‘AAA’ => ‘K’, # Lysine
‘AAG’ => ‘K’, # Lysine
‘AGC’ => ‘S’, # Serine
‘AGU’ => ‘S’, # Serine
‘AGA’ => ‘R’, # Arginine
‘AGG’ => ‘R’, # Arginine
‘CCC’ => ‘P’, # Proline
‘CCG’ => ‘P’, # Proline
‘CCU’ => ‘P’, # Proline
‘CAC’ => ‘H’, # Histidine
‘GUA’ => ‘V’, # Valine
‘GUC’ => ‘V’, # Valine
‘GUG’ => ‘V’, # Valine
‘GUU’ => ‘V’, # Valine
‘GCA’ => ‘A’, # Alanine
‘GCC’ => ‘A’, # Alanine
‘GCG’ => ‘A’, # Alanine
‘GCU’ => ‘A’, # Alanine
‘GAC’ => ‘D’, # Aspartic Acid
‘GAU’ => ‘D’, # Aspartic Acid
‘GAA’ => ‘E’, # Glutamic Acid
‘GAG’ => ‘E’, # Glutamic Acid
‘GGA’ => ‘G’, # Glycine
‘GGC’ => ‘G’, # Glycine
‘GGG’ => ‘G’, # Glycine
‘GGU’ => ‘G’ # Glycine
);
my ($protein) = “”;
for(my $i=0;$i {
$codon = substr($rna,$i,3);
$protein .= $genetic_code{$codon};
}
print “Translated protein sequence is $protein”;
<>;

This program can also used for six reading frame, by changing the three character shift in forward and reverse of the RNA sequence.

Doing Simulation using Discovery Studio 2.1

Ashok Kumar — Sat, 20 Feb 2010 23:29:45 +0000

The protocols and tools under Simulation allow you to run energy calculations, solvation, energy minimization, and molecular dynamics simulations using the CHARMm and other programs.

The protocols under Simulation serve the following types of users:

Novice protein modelers and computational chemists who are interested primarily in running pre-defined simulation protocols to provide simple minimization or dynamics of the molecular structure under study. Novice protein modelers and computational chemists will find that the protocols are an easy way to run predetermined workflows with a minimal amount of configuration.
Expert protein modelers and computational chemists who are interested in running several simulation steps independently and trying out different parameterizations.

Analysis Goals

You can use Simulation methods to:

Analyze molecular trajectories
Calculate energies using molecular mechanics or QM-MM based methods
Calculate interaction energies
Equilibrate a molecule with molecular dynamics
Perform a dynamics simulation to adjust the temperature of a molecule
Perform molecular dynamics on a pre-equilibrated molecule
Minimize a molecule using molecular mechanics or QM-MM
Calculate the radial distribution function for two sets of atoms in a trajectory
Solvate a system by adding water molecules
Perform a set of minimization and equilibration steps followed by molecular dynamics
Calculate fundamental motions (Principal Components) of a trajectory
Prepare structures for simulation using the forcefield tools
Apply constraints on atoms in structures before performing simulation analysis
Analyze molecular trajectories

Simulation Tasks

The following table describes the basic tasks that are possible with the Simulation methods. Read more..

Protein Modeling using Discovery Studio 2.1

Ashok Kumar — Mon, 18 Jan 2010 15:53:19 +0000

Experimental structure determination involves difficult methods that require a significant amount of expertise and resources. Protein Modeling on the other hand enables access to sensible structural models in much shorter periods of time. The major aim of protein modeling is the prediction of a protein’s tertiary structure from its primary structure. To this end a diverse range of approaches have been developed comparative, de novo or ab initio structure prediction.

The protein modeling methods provided in Discovery Studio provide an extensive set of tools for the construction of molecular structures and analysis of their behavior.

Protein Modeling in Accelrys Discovery Studio 2.1

Analysis Goals

Protein Modeling provides tools and protocols that allow you to:

Build and edit proteins or peptides
Modify protein structures and generate reports of protein structures
Identify and report abnormalities in a protein structure
Align sequences according to sequence similarity or structure similarity
Build homology models for a protein sequence
Refine side-chain conformation of a protein structure
Refine conformation of one or more loop regions of a protein structure
Mutate residues and optimize structure
Predict protein docking conformations
Model antibody structure and variable loop conformations
Analyze the sequence conservation pattern of a sequence family
Identify conserved functional patches in a protein structure

Protein Modeling Tasks

The following table describes the basic tasks that are possible with the Protein Modeling methods in Discovery Studio. Click here for tutorial….

Running JAVA program in Linux Ubuntu

Ashok Kumar — Wed, 16 Dec 2009 15:49:39 +0000

Steps to run JAVA program in Ubuntu:

1. Go to Applications > Accessories > Terminal, to open terminal window.

2. Type the following in command line

gedit Add.java

3. Enter the code bellow in the editor.

/* Addition of two numbers – Add.java */
import java.io.*;
class Add
{
public static void main(String args[])
{
InputStreamReader ISR = new InputStreamReader(System.in);
BufferedReader BR = new BufferedReader(ISR);
int a = 0, b = 0;
try
{
System.out.print(”Enter the first number: “);
a = Integer.parseInt(BR.readLine());
System.out.print(”Enter the second number: “);
b = Integer.parseInt(BR.readLine());
}
catch(Exception e)
{
System.out.println(”Check the program.”);
}
System.out.println(”Addition of ” + a + ” + ” + b + ” is” + (a+b));
}
}

4. Save the file and close to return to terminal window.

5. Firstly compile the code using the following command

javac Add.java

That would produce an class file you may need to run the program.

7. Now run this executable using the following command

java Add

8. Output should show as follows

Enter the first number: 49
Enter the second number: 2
Addition of 49 + 2 is 51

Note: If java is not present in the system, download it through terminal window using command sudo apt-get install sun-java6-bin sun-java6-jre sun-java6-jdk

Installing and Configuring XAMPP in Windows 7

Ashok Kumar — Mon, 14 Dec 2009 16:29:30 +0000

Many people know from their own experience that it’s not easy to install an Apache web server and it gets harder if you want to add MySQL, PHP and Perl.

XAMPP is an easy to install Apache distribution containing MySQL, PHP and Perl. XAMPP is really very easy to install and to use – just download, extract and start.

At the moment there are four XAMPP distributions:

XAMPP for Linux

The distribution for Linux systems (tested for SuSE, RedHat, Mandrake and Debian) contains: Apache, MySQL, PHP & PEAR, Perl, ProFTPD, phpMyAdmin, OpenSSL, GD, Freetype2, libjpeg, libpng, gdbm, zlib, expat, Sablotron, libxml, Ming, Webalizer, pdf class, ncurses, mod_perl, FreeTDS, gettext, mcrypt, mhash, eAccelerator, SQLite and IMAP C-Client.

XAMPP for Windows

The distribution for Windows 2000, 2003, XP and Vista. This version contains: Apache, MySQL, PHP + PEAR, Perl, mod_php, mod_perl, mod_ssl, OpenSSL, phpMyAdmin, Webalizer, Mercury Mail Transport System for Win32 and NetWare Systems v3.32, Ming, JpGraph, FileZilla FTP Server, mcrypt, eAccelerator, SQLite, and WEB-DAV + mod_auth_mysql.

XAMPP for Mac OS X

The distribution for Mac OS X contains: Apache, MySQL, PHP & PEAR, SQLite, Perl, ProFTPD, phpMyAdmin, OpenSSL, GD, Freetype2, libjpeg, libpng, zlib, Ming, Webalizer, mod_perl.

XAMPP for Solaris

The distribution for Solaris (developed and tested with Solaris 8, tested with Solaris 9) contains: Apache, MySQL, PHP & PEAR, Perl, ProFTPD, phpMyAdmin, OpenSSL, Freetype2, libjpeg, libpng, zlib, expat, Ming, Webalizer, pdf class. WARNING: This version of XAMPP is still in the first steps of development. Use at you own risk!

Easy installation and deinstallation

To install XAMPP you only need to download and extract XAMPP, that’s all. There are no changes to the Windows registry (not true if you use the Windows installer version of XAMPP) and it’s not necessary to edit any configuration files. It couldn’t be easier!To check that XAMPP is working some sample programs are included, there is a small CD collection program (written in PHP using MySQL) and a small guest book software (written in Perl) and several other demonstration utilities.

If you decide that XAMPP isn’t needed any more just delete the XAMPP directory and it’s completely removed from your system.

However if you use the Windows installer version of XAMPP it’s recommended to use the uninstall feature. As every installer the installer will make registry entries to remember the install.

Steps to install:

Step 1:

Step 2:

Step 3:

Step 4:

Step 5:

Step 6:

Step 7:

Step 8:

Step 9:

Step 10:

Step 11:

Step 12:

Step 13:

Step 14:

After changing to new password, open C:\xampp\phpMyAdmin\config.inc.php in a text editor. Go to line 21 [$cfg['Servers'][$i]['password'] = ”;] and change it to new password [$cfg['Servers'][$i]['password'] = ‘new_password’;].

Two methods to run PHP script

Ashok Kumar — Tue, 08 Dec 2009 16:54:53 +0000

HTML with PHP :-

HTML: add.htm

Adding two numbers

Enter the first number:

Enter the second number:

PHP: add.php

Adding two numbers

$a=$_POST["a"];

$b=$_POST["b"];

$c=$a+$b;

print “Addition of $a and $b is $c.”;

Only with PHP :-

$a = $_POST["a"];

$b = $_POST["b"];

if (!isset($_POST['add']))

{ // If page is not submitted to itself echo the form

Adding Two Numbers

Enter the first number:

Enter the second number:

}

else

{

$c=$a+$b;

print “Addition of $a and $b is $c.”;

}

HTML with PHP :-

HTML: add.htm

Adding two numbers

PHP: add.php

Adding two numbers

$a=$_POST["a"];
$b=$_POST["b"];
$c=$a+$b;
print “Addition of $a and $b is $c.”;
?>

Only with PHP :-

$a = $_POST["a"];
$b = $_POST["b"];
if (!isset($_POST['add']))
{ // If page is not submitted to itself echo the form
?>

Adding Two Numbers

}
else
{
$c=$a+$b;
print “Addition of $a and $b is $c.”;
}
?>

Linux wvdial.conf script for Vodafone IN

Ashok Kumar — Tue, 08 Dec 2009 16:37:46 +0000

[Modem0]

Modem = /dev/rfcomm0

Baud = 115200

SetVolume = 0

Dial Command = ATDT

Init1 = ATZ

Init3= ATM0

FlowControl = CRTSCTS

[Dialer vodafone]

Username = “vodafone”

Password = “vodafone”

Phone = *99#

Stupid Mode = 1

Init1 = ATZ

Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0

Init3 = AT+CGDCONT=1,”10.10.1.100:9401″,”portalnmms”,”",0,0

Inherits = Modem0

[Dialer three]

Username = “none”

Password = “none”

Phone = *99#

Stupid Mode = 1

Init1 = ATZ

Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0

Init3 = AT+CGDCONT=1,”10.10.1.100:9401″,”portalnmms”,”",0,0

Inherits = Modem0

[Modem0]

Modem = /dev/rfcomm0

Baud = 115200

SetVolume = 0

Dial Command = ATDT

Init1 = ATZ

Init3 = ATM0

FlowControl = CRTSCTS

[Dialer vodafone]

Username = “vodafone“

Password = “vodafone“

Phone = *99#

Stupid Mode = 1

Init1 = ATZ

Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0

Init3 = AT+CGDCONT=1,”10.10.1.100:9401“,”portalnmms“,”",0,0

Inherits = Modem0

[Dialer three]

Username = “none“

Password = “none“

Phone = *99#

Stupid Mode = 1

Init1 = ATZ

Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0

Init3 = AT+CGDCONT=1,”10.10.1.100:9401“,”portalnmms“,”",0,0

Inherits = Modem0

Running C or C++ program in Linux

Ashok Kumar — Fri, 04 Dec 2009 02:11:57 +0000

Steps to run C program in Ubuntu:

1. Go to Applications > Accessories > Terminal, to open terminal window.

2. Type the following in command line

sudo gedit first.c

3. Enter the code bellow in the editor.

/* Program first.c */
#include
main()
{
printf(”Hello World.\n”);
}

4. Save the file and close to return to terminal window.

5. Firstly compile the code using the following command

cc -c first.c

That would produce an object file you may need to add to the library.

6. Then create an executable using the following command

cc -o first first.c

7. Now run this executable using the following command

./first

8. Output should show as follows

Hello World.

Steps to run C++ program in Ubuntu:

1. Go to Applications > Accessories > Terminal, to open terminal window.

2. Type the following in command line

sudo gedit first.cpp

3. Enter the code bellow in the editor.

/* Program first.cpp */
#include
main()
{
std::cout<<”Hello World.”< }

4. Save the file and close to return to terminal window.

5. Now compile the code using the following command

g++ first.cpp -o second

6. Then run this executable using the following command

./second

7. Output should show as follows

Hello World.

A sample factorial program in C

/* Factorial using C */
#include
int main()
{
int i,n,f=1;
printf(”\nEnter the number: “);
scanf(”%d”,&n);
for(i=1;i<=n;i++)
{
f=f*i;
}
printf(”\nFactorial of %d is %d \n\n”,n,f);
}

Output:

$ sudo gedit factorial.c
$ cc -c factorial.c
$ cc -o factorial factorial.c
$ ./factorial

Enter the number: 6
Factorial of 6 is 720