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Frequency Plot of Protein Sequences using R

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A frequency plot is a graphical data analysis technique for summarizing the distributional information of a variable. The response variable is divided into equal sized intervals (or bins). The number of occurrences of the response variable is calculated for each bin. In this tutorial, the number of occurrences of each amino acids in the protein sequence (response variable) is calculated and sorted in ascending order. The frequency plot then consists of: Vertical Axis = Amino acids Horizontal Axis = Frequencies of the amino acids There are 4 types of frequency plots: Frequency plot (absolute counts); Relative frequency plot (convert counts to proportions); Cumulative frequency plot; Cumulative relative frequency plot. The frequency plot and the histogram have the same information except the frequency plot has lines connecting the frequency values, whereas the histogram has bars at the frequency values. Frequency plot using R In this tutorial, the programming language R and...
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DotPlot for Protein Sequences using R

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Dotplot is the visual representation of the similarity between two protein or nucleotide sequences. Dotplot was introduced by Gibbs and McIntyre in 1970 and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical ( y ) and horizontal ( x ) axes. Individual cells in the matrix can be shaded black if residues are identical, so that matching sequence segments appear as runs of diagonal lines across the matrix. The closeness of the sequences in similarity will determine how close the diagonal line is to what a graph showing a curve demonstrating a direct relationship is. This relationship is affected by certain sequence features such as frame shifts , direct repeats , and inverted repeats . Frame shifts include insertions, deletions, and mutations. The presence of one of these features, or the presence of multiple features, will cause for multiple lines to be plotted in a various possibility of configurations, depending on the features pre...
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Bioinformatics Carrer Opportunities

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Bioinformatics is the somewhat new and rather unfortunate term that is commonly employed for referring to the use of computers in biological research. Bioinformatics now looks like a hot cake. The number of jobs advertised for bioinformatics in Nature and Science magazine has increased by 96% bioinformatics job advertisements. According to the U.S. Bureau of Labor Statistics (BLS), the median annual salary for biological scientists, including bioinformatics scientists, was about $71,000 in 2011. Expected job growth for scientists in this category (including biochemists and biophysicists) is 31% between 2010 and 2020. According to BLS data, bioinformatics technicians are included under the umbrella of statistical assistants, whose mean salary was about $39,000 in 2011. The Department of Labor reports bioinformatics technicians will have job growth of 3% to 9% between 2010 and 2020. According to PayScale.com , however, the median salary for biotechnology research scientists with bioin...
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Find and Delete Core Dumps using PHP and Shell

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Linux sometimes dumps a huge file when a script crashes. These core files can build up and eat away valuable disk space. Some other methods of deleting core files will damage your server. Here are a few simple commands I use to find and delete these core dump files safely.
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Replacing form fields by text in PHP

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In PHP, the form field has replaced with the custom text after processing by either using an HTML file or hiding the form fields using the PHP script. This method can also be used for applying static header and footer on the web page. In the following example, I have used an HTML file and PHP script to add two numbers. The HTML file content has replaced during the execution. Before Execution After Execution Source Code: form.html <form method="post" action="<?php print $_SERVER['PHP_SELF']; ?>" > First Number: &nbsp;&nbsp;&nbsp;&nbsp;<input type="text" name="first"><br> Second Number: <input type="text" name="second"><br><br> <input type="reset" value="Reset"><input type="submit" value="Submit"> </form> addition.php <html> <head> <title>Adding two number...
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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

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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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