BioGem Blog

Hydrophobicity is the property of being water repellent, tending to repel and not absorb water. Calculation of hydrophobicity in proteins is important in identifying its various features. This can be membrane spanning regions, antigenic sites, exposed loops or buried residues. Usually, these calculations are shown as a plot along the protein sequence, making it easy to identify the location of potential protein features. The hydrophobicity is calculated by sliding a fixed size window (of an odd number) over the protein sequence. At the central position of the window, the average hydrophobicity of the entire windows is plotted. A hydrophobicity plot is a quantitative analysis of the degree of hydrophobicity of amino acids of a protein. It is used to characterize or identify possible structure or domains of a protein. The plot has amino acid sequence of a protein on its x-axis, and degree of hydrophobicity on its y-axis. In hydrophobicity plot, the degree of hydrophobicity is tak...

Introduction to 2D Smooth Graph Connecting line between two points ( x 1 , y 1 ) and ( x 2 , y 2 ) is known as a graph. A non-uniform cartesian co-ordinates points will generate a rigid line, which looks ugly. In Python, a rigid graph can be regenerated into a smooth graph by interpolating more points using SciPy module. SciPy (Scientific Python library) generates more sub-points based on the input array values to form a smooth curve. In this program, I have used input() function to get n number of points ( x , y ) from the user through keyboard ( screenshot is given in the bottom ) and store it to arrays. The co-ordinates points used in the program are (1, 2), (2, 5), (3, 3), (4, 6), (5, 7), (6, 2), (7, 10), (8, 5), (9, 6), and (10, 3). Program Implementation In this tutorial, I have used Python 3.5.2 (64-bit) software, and 7 modules: MatPlotLib 2.0.2 , PyParsing 2.2.0 , Python-DateUtil 2.6.1 , PyTZ 2017.2 , SetupTools 36.2.0 , Cycler 0.10.0 , SciPy 0.19.1 , and NumPy-MKL 1.13...

Introduction to Polynomial Graph Polynomial curve a is smooth and continues line of graph, connected by a series of co-ordinates calculated using a polynomial equation (For example, y = f ( x ), where f ( x ) = A x 2 + B x + C). In this program, I have used a polynomial equation y = 3 x 2 + 4 x + 2 with x values range from 0 to 5. The program generated co-ordinate points ( x , y ) in the graph will be (0, 2), (1, 9), (2, 22), (3, 41), (4, 66), and (5, 97). Program Implementation In this tutorial, I have used Python 3.5.2 (64-bit) software, and 7 modules: MatPlotLib 2.0.2 , PyParsing 2.2.0 , Python-DateUtil 2.6.1 , PyTZ 2017.2 , SetupTools 36.2.0 , Cycler 0.10.0 , and NumPy-MKL 1.13.1 implemented in Windows 10 Enterprise operating system. The 7 modules are chosen based on the compatibility of Python and OS version and bit. Source Code import numpy as np import matplotlib.pyplot as plt a = 3 b = 4 c = 2 x = np.linspace(0, 10, 256, endpoint = True) y = (a * (x * x)) + (b ...

Introduction to Sine/Cosine Graph The sine and cosine graphs are almost identical, except the cosine curve ( y = cos ( x )) starts at amplitude y = 1, when angle x = 0° (whereas the sine curve ( y = sin ( x )) starts at amplitude y = 0). We say the cosine curve is a sine curve which is shifted to the left by 90°. The graph of sine and cosine is like a wave that forever oscillates between -1 and 1, in a shape that repeats itself every 360° (2π) units. Program Implementation In this tutorial, I have used Python 3.5.2 (64-bit) software, and 7 modules: MatPlotLib 2.0.2 , PyParsing 2.2.0 , Python-DateUtil 2.6.1 , PyTZ 2017.2 , SetupTools 36.2.0 , Cycler 0.10.0 , and NumPy-MKL 1.13.1 implemented in Windows 10 Enterprise operating system. The 7 modules are chosen based on the compatibility of Python and OS version and bit. Source Code import numpy as np import matplotlib.pyplot as plt X = np.linspace(-np.pi, np.pi, 256, endpoint = True) C, S = np.cos(X), np.sin(X)...

Introduction to Exponential Graph Exponential curve a is smooth and continues line of graph, connected by a series of co-ordinates calculated using a polynomial equation containing variable exponential value (For example, y = f ( x ), where f ( x ) = A e B x + C). In this program, I have used a polynomial equation with a exponential variable y = 5 e -2 x + 1 with x values range from 0 to 10. The program generated co-ordinate points ( x , y ) in the graph will be (0, 6.0), (1, 1.7), (2, 1.1), (3, 1.0), (4, 1.0), (5, 1.0), (6, 1.0), (7, 1.0), (8, 1.0), (9, 1.0), and (10, 1.0). Program Implementation In this tutorial, I have used Python 3.5.2 (64-bit) software, and 7 modules: MatPlotLib 2.0.2 , PyParsing 2.2.0 , Python-DateUtil 2.6.1 , PyTZ 2017.2 , SetupTools 36.2.0 , Cycler 0.10.0 , and NumPy-MKL 1.13.1 implemented in Windows 10 Enterprise operating system. The 7 modules are chosen based on the compatibility of Python and OS version and bit. Source Code import numpy as...

This tutorial explains about a simple method to configure Apache, PHP, MySQL, Perl and Python in windows platform. In this tutorial, I have used the latest operating system (Windows 8.1 Enterprise Edition 64-bit) and latest softwares - XAMPP 1.8.3 and Python 3.3.0. Refer official site of XAMPP and Python for installation instructions. XAMPP is an easy to install Apache distribution containing MySQL, PHP and Perl. The XAMPP 1.8.3 contains of 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, FileZilla FTP Server, mcrypt, eAccelerator, SQLite, and WEB-DAV + mod_auth_mysql. The default configuration of Apache is perfectly linked with MySQL, PHP and Perl. Since Perl and Python run under common gateway interface (CGI), configuring Python CGI with XAMPP is very easy. To convert XAMPP into XAMPPP, we have to change the existing AddHandler Apache configuration command to AddHa...

This is a simple tutorial for computing smallest of two numbers using the classes and objects in C++. In this tutorial, I have used Dev C++ v5.11 software for compiling the C++ program. Classes and Objects in C++ In C++ language, Object Oriented Programming (OOP) is a concept introducted to class ify or organize data into objects. A class is a user defined type or data structure declared with keyword class that has data and functions (also called methods) as its members whose access is governed by the three access specifiers private , protected or public (by default access to members of a class is private ). The private members are not accessible outside the class; they can be accessed only through methods of the class. The public members form an interface to the class and are accessible outside the class. Instances of a class data type are known as objects and can contain member variables, constants, member functions, and overloaded operators defined by the programmer. Sour...