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Molecular Graphics Models using Swiss PDB Viewer

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This tutorial presents various models of molecular graphics representations such as Wireframe model, Ball & Stick model, Spacefill model, Surface model, Stick model, Backbone model, Van der Waals model, Ribbon model, Strand model, and Electrostatic potential model of protein structure using Swiss PDB Viewer . Protocol Open Swiss PDB Viewer software. Click File → Open PDB File… menu to browse protein structure (. pdb file) location. By default, it displays protein structure in “ Wireframe ” model. In Control Panel window, right-click symbol “ ::v ” to display whole protein structure in “ Van der Waals ” model. Click Display → Render in Solid 3D menu, and click Display → Show Backbone Oxygens menu (deselect) to display protein structure in “ Sticks ” model. In Control Panel window, right-click symbol “ side ” to display whole protein structure in “ Backbone ” model. In Con...
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Bouncing Text Animation Effect using Pure CSS

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This is a simple tutorial for creating bouncing text animation effect using pure CSS3 and HTML. In this tutorial, I have used CSS3 animation property with value ease to move text ( keyframe ) towards top and bottom ( alternate -- distance -10px ) at 1 second rate infinitely ( infinite ). Source Code HTML: index.html <!DOCTYPE html> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <title>Bouncing Text Animation Effect</title> <link href="style.css" rel="stylesheet" type="text/css" /> </head> <body> <div id="title_wrapper"> <div id="text"> <i>B</i><i>o</i><i>u</i><i>n</i><i>c</i><i>i</i><i>n</i><i>g...
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Music Search using Google Assistant in Android

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The Google Assistant app allows you to quickly access your smartphone assistant by pressing and holding down your home button or by simply saying, “Ok Google.” It can open your smartphone apps by passing system commands to your Android operating system. Google is a world's most popular search engine. It is highly famous for keyword search, and image search. Google's voice recognition feature allows searching music or videos by matching the sound. This feature can be simply accessed from Android smartphones through Google Assistant by entering the keywords (or voice) “(What|Find|What's|etc.)” and “(Song)”. For example, “what song”. This is a simple tutorial for searching music from Google through Google Assistant. Accessing Google Assistant Download Google Assistant app from Google Play Store, if you do not have in your smartphone. Open the Google Assistant app and press the keypad icon. Now enter the keyword ...
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NCBI BLAST Graphical Summary using HTML/CSS

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This is a simple tutorial for designing a webpage for displaying the graphical summary of biological sequence alignment similar to the output of the NCBI BLAST+ program using HTML and CSS languages. In this tutorial, I have given few example hits (in bars) that match all range of bit scores (mentioned by color key). NCBI BLAST Graphical Summary NCBI BLAST is a most popular bioinformatics framework for finding local similarity between two or more biological sequences. It addresses a fundamental problem in bioinformatics research. The heuristic algorithm it uses is much faster than other approaches, such as calculating an optimal alignment. This emphasis on speed is vital to making the algorithm practical on the huge genome databases currently available, although subsequent algorithms can be even faster. In NCBI BLAST, the graphic is an overview of the database sequences aligned to the query sequence. These are represented horizontal bars colored coded by score and showing the ex...
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ATCG Content of Multiple Gene Sequences using C++

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This is a simple tutorial for computing ATCG contents of multiple gene sequences using the classes, objects, and members in C++. In this tutorial, I have used Dev C++ v5.11 software for compiling the C++ program. Program Design A. Define a class to represent a gene sequence data. Include the following members: Data members: Gene name Gene ID Length A, T, G, C content Member functions: To read data for a gene To compute A, T, G, C content To display all the details of a gene B. Write a main program to test the program by reading n gene sequences data. Source Code /* Computing ATCG Content of Multiple Gene Sequences */ #include <iostream> #include <iomanip> #include <conio.h> #include <string.h> #include <stdlib.h> class gene { char r, gene_name[20][20], gene_seq[20][200], gene_id[20][20], id[20]; int gene_length, a, t, c, g, o, n, i, j, m, substr_eq, substr_rem; std::str...
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Biological Sequence Pattern Matching using Perl

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This article is a simple Perl programming tutorial for matching patterns in the biological sequence using regular expressions. In this tutorial, I have used ActiveState Perl 5.24.3 software for compiling the Perl script. Pattern Matching In Bioinformatics, string matching or pattern matching is a fundamental and popular method used in a wide range of applications ranging from sequence alignment to functional prediction. Pattern matching is classified into exact pattern matching and approximate pattern matching. The exact pattern matching method does not allow any insertion, deletion, or substitution of characters while matching with the target sequence, whereas the approximate pattern matching method allows with certain limitations. In Computational Biology, a pattern is an expression as a sequence of characters with a defined set of symbolic representation. Example: N{P}-[ST]{P}A(2,3). Source Code system('cls'); print "\n+-----------------------------------+...
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Computing Amino Acid Composition using C++

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This article explains the simple method to compute composition of amino acids in the protein sequence using C++. In this tutorial, I have used Dev C++ v5.11 software for compiling the C++ program. Length of the Protein Sequence Length of the protein sequence is the count ( C ) of the total number of amino acid characters in the protein sequence. Let, Protein Sequence (S) = S 1 S 2 S 3 …S l -1 S l Where, S ∈ {A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y} Then, l is the length of the protein sequence (S). Amino Acid Composition of the Protein Sequence Amino acid composition is the sum of count ( C ) of each amino acids in the protein sequence. Count of each amino acids is C A , C C , C D , C E , C F , C G , C H , C I , C K , C L , C M , C N , C P , C Q , C R , C S , C T , C V , C W , and C Y . Source Code // Computing Composition of Amino Acids in the Protein Sequence #include <iostream> #include <iomanip> #include <stri...
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