BioGem Blog

This is a simple tutorial which explains how to design your own web interface for NCBI BLAST+ to perform local and online database search using PHP in webserver. The PHP library loc BLAST executes the NCBI BLAST+ programs using exec() function through passing parameters from the HTML form fields. In loc BLAST , two list boxes were used to select program & database, and text area & file upload is used to input query sequence in the FASTA file format. A FASTA file validation function is included to validate the query sequence before executing the BLAST programs. The loc BLAST PHP library and test database files were freely available at GitHub . Requirements for loc BLAST Setup In this tutorial, I have given a brief explanation about embedding the latest NCBI BLAST+ (the latest version of NCBI BLAST+ as on November 17, 2020 is 2.11.0 .) in any PHP enabled web server. The latest version of NCBI BLAST+ (standalone command-line BLAST programs) can be downloaded from the FTP s...

This is a simple tutorial which explains how to safely extract multiple sequences from a FASTA file using PHP script. I have used four functions to perform different tasks: read_fas_file() - to check invalid file, fas_check() - to check FASTA file format, get_seq() - to retrieve sequence and sequence name pairs, and fas_get() - to extract and display multiple FASTA file formatted sequences. The full source code and multiple protein sequences in FASTA file format used in this tutorial is given below. Source Code function read_fas_file($x) { // Check for Empty File if (!file_exists($x)) { print "File Not Exist!!"; exit(); } else { $fh = fopen($x, 'r'); if (filesize($x) == 0) { print "File is Empty!!"; fclose($fh); exit(); } else { $f = fread($fh, filesize($x)); fclose($fh); return $f; } } } function fas_check($x) { // Check FASTA File Format $gt = substr($x, 0, 1); if ($gt != ">") { print "Not F...

This is a simple tutorial which explains how to show or hide lines in a paragraph using JavaScript. The concept is to split the lines in the paragraph into two sections and show/hide the second section by clicking a hyperlinked text (to create a toggle effect). By default, the first section in the paragraph is set to always visible, and a hyperlink at the end of the line with onclick action to display the second section . Similarly, a hyperlink at the end of the line of the second section with onclick action is displayed after a mouse click event to hide the second section . Example This is a simple tutorial which explains how to show or hide lines in a paragraph using JavaScript. <a style = 'text-decoration: none' id = 'show_line' href = 'javascript:void(0)' onclick = "document.getElementById('more').style.display = 'inline'; document.getElementById('hide_line').style.display = 'inline'; document.getElemen...

Pointing Subdomain to another Domain Pointing a subdomain to another domain is a challenging task for those who shift to another hosting provider. The problem is, old domain must point to the new domain properly for all sub-directories (Eg. https://sub.site1.com/article/introduction.html to https://www.site2.com/article/introduction.html ). If the subdomain does not properly points to the new domain, the link may get broken. We can point a subdomain to another domain through cPanel, Zone Editor, or .htaccess file. In this tutorial, I have used cPanel version 66.0.14 to take screenshot. cPanel Method It is an easy method to point a subdomain to another domain. In this method, we can simply set both domains in cPanel to perform the task. In the Domains section of cPanel, click the Redirects link. In the Redirects page, enter the old subdomain and the new domain as shown in the screenshot below. Select the Wild Card Redirect box to redirect all files within a directory with th...

Introduction to PyMOL PyMOL is a Python-enhanced OpenGL based molecular visualization tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is available at SourceForge.net ( https://sourceforge.net/projects/pymol/ ) for free to everyone. The commercial graphical end PyMOL is developed, maintained and distributed by Schrödinger, Inc ( https://www.pymol.org/ ). PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL. Requirements for PyMOL Installation In this tutorial, I have explained how to install the latest PyMOL software (the latest version of PyMOL software as on September 15, 2016 is 1.8.3.2) for free. I have chosed Windows 10 Enterprise OEM 64-bi...

1.You have been asked to review instructions in a .PDF file, but the file doesn't open. What is a typical troubleshooting step for this issue? Reinstall or update Adobe Reader Ask for another copy of the file Open the file with Notepad Convert the file to a different format 2. In Windows Vista, Windows 7, or Windows 8, what is the Snipping Tool used for? To create audio snippets To crop photos uploaded from a camera To edit movies To capture and create screenshots 3. An application is not responding; how would you force the application to close? Restart the computer Click on the red X icon on the application Open the task manager, select the application, and click End Task Open Programs and Features, select the application, and click Uninstall 4. In Windows Vista, Windows 7, and Windows 8 where are recently downloaded files stored by default? C:\Users\username\Downloads\ C:\Documents and Settings\username\Downloads\ C:\Program Files\ C:\P...

Most of the windows users choose XAMMP to install Apache distribution containing MySQL, PHP, phpMyAdmin, and Perl. But, if you try to update any one of the softwares, you may face difficulties. Either you must have to install the latest version of XAMPP (or) you must update the software and configure the web server manually. In such case, we may either loss the data (or) it may remain nonfunctional. So it is safe to take backup of whole files, before trying to install manually. In this tutorial, I have tried to update the old phpMyAdmin in the XAMPP to phpMyAdmin 4.2.12 ( the latest stable release, as on Nov 29, 2014 ) and faced many technical problems. I searched through google for this issue, but I didn't got a proper solution. Finally, I referred the phpMyAdmin error message and documentations and solved the problem. It works fine now. The simple and easy steps which I followed is explained below: Download the latest version of the phpMyAdmin from the official site ht...