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Running Swiss-PdbViewer on Ubuntu

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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 ...
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Embedding Perl into Perl

This article describes embedding a Perl script into a Perl script. The program executes through Common Gateway Interface (CGI), which reads ASCII file through file upload method 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 other system programs too. file-upload.html <html> <head> <title>File Upload</title> </head> <body> <form method="post" action="/cgi-bin/file-upload.pl" enctype="multipart/form-data"> Enter the file to upload:<br> <input name="file" size="45" type="file"><br> <p> <input name="reset" type="reset"> <input name="submit" value="Upload" type=...
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RNA to Protein Translation in PERL

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In PERL programming, an RNA sequence can be translated to a protein sequence by substituting equivalent amino acid characters to triplet characters of RNA. This method has followed to find six reading frames (three in the forward direction, and three in the reverse direction). In this program, I have used the associative array (also known as a hash array) to associate triplet characters with amino acid characters. The associate array corresponding to codon table is arranged to 20 amino acid character. The triplet codon table is shown below: 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...
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Sir Isaac Newton's 367th Birthday

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On 4 January 2010, Google Doodle celebrated Sir Isaac Newton's 367th Birthday, as he was born on January 4, 1643. His birthdate is sometimes also marked as December 25, 1642, due to England's use of the Julian calendar at the time. This celebrated English physicist and mathematician, known for his work on gravity and laws of motion, is a key figure in the Scientific Revolution. Today on the Google home page, an animated apple is falling, over and over, with a satisfying plunk—a 367th birthday tribute to Sir Isaac Newton. Legend has it that Isaac Newton formulated gravitational theory in 1665 or 1666 after watching an apple fall and asking why the apple fell straight down, rather than sideways or even upward. "He showed that the force that makes the apple fall and that holds us on the ground is the same as the force that keeps the moon and planets in their orbits," said Martin Rees, President of Britain's Royal Society, the United Kin...
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Running JAVA program in Linux Ubuntu

The tutorial bellow explains simple procedure to compile, interpret, and execute Java program in Ubuntu using JDK sofware. 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)...
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Linux wvdial.conf script for Vodafone IN

[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
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Two methods to run PHP script

This article explains different methods to write PHP scripts. Basically PHP is a HTML, without using PHP script in it. A PHP script can be inserted between <?php and ?> tags. General contents can be simply displayed using HTML web page to reduce PHP server script runtime duration. HTML and PHP HTML: add.html <html> <head> <title>Addition of Two Numbers</title> </head> <body> <form action="add.php" method="post"> Enter the first number: <input type="text" name="a"><br/> Enter the second number: <input type="text" name="b"><br/> <input type="submit" name="submit" value="ADD"> </form> </body> </html> PHP: add.php <html> <head> <title>Addition of Two Numbers</title> </hea...
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