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Bioinformatics Protocol for NGS Data Analysis

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A step-by-step Bioinformatics protocol for Next-Generation Sequencing (NGS) are, Data quality control using tools like FastQC to assess raw data. Data preprocessing for adapter trimming and low-quality base removal with tools like Trimmomatic or FastP. Read mapping to a reference genome using aligners such as BWA or Bowtie2. Post-alignment processing including duplicate removal with Picard and variant calling with GATK or Samtools. Downstream analysis and visualization for specific applications like differential gene expression or variant interpretation using tools like R packages or IGV. A more detailed breakdown of those were given below 1. Data Quality Control (QC) Purpose: To check the quality of the raw sequencing reads and identify any potential issues. Tools: FastQC: A widely used tool to generate quality control reports for raw sequencing data. Output: A report summarizing metrics like Phred scores, adapter contamination, and sequence qu...
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Creating 2D Line Plot using GNU Plot Software

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A simple Gnuplot script designed to generate a customized 2D line plot of potential energy data (presumably vs. simulation steps or time), using data from a file named PE.txt (available in GitHub ). The script applies several visual formatting settings to make the plot visually appealing and informative. This script produces a clean, stylized 2D plot of potential energy vs. simulation steps with (1) custom fonts, colors, and line styles, (2) no legend, (3) margins around the x-axis, and (4) automatic y-axis scaling. Source Code set title '{/Times-New-Roman=14:Bold Potential Energy Plot}' tc rgb '#167116' set xlabel '{/Arial:Italic Number of steps}' tc rgb 'red' set ylabel '{/Arial:Italic Potential energy}' tc rgb 'red' set style line 1 lt 1 lc rgb '#f70453' lw 0.5 set grid layerdefault lt 0 lc rgb 'blue' lw 0.5 set border lt 1 lc rgb 'blue' lw 1 unset key plot 'PE.txt' with lines ls 1 set xrang...
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Molecular Dynamics Simulation of Micromolecules using Chimera

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Performing a Molecular Dynamics (MD) simulation of a small molecule in UCSF Chimera involves a series of steps to prepare the molecule, set up the simulation environment, run the simulation, and finally, analyze the resulting trajectory. Here's a step-by-step guide for the same: 1. Loading and Preparing the Small Molecule Structure Open Chimera: Launch UCSF Chimera or ChimeraX. Load your molecule: Import your small molecule structure into Chimera using File > Open or File > Fetch by ID if the structure is available in a database like the Protein Data Bank (PDB). Add Hydrogens: Use the "Molecular Dynamics Simulation" tool's "Prep Structure" section to add hydrogens. You might also be able to use the addh command. Assign Force Field Parameters: Since you are working with a small molecule (a nonstandard residue), you will use Amber's Antechamber module, which is included in Chimera, to assign force field parameters. This involves ass...
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Constructing Phylogenetic Tree using UPGMA Method

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UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a distance-based method for constructing phylogenetic trees. It works by iteratively clustering the two closest groups of sequences together, forming a new cluster until all sequences are grouped into a single tree. The distances between clusters are calculated using the average of all pairwise distances between sequences within those clusters. UPGMA produces rooted trees, meaning it has a defined root representing the common ancestor. Here's a more detailed explanation: 1. Distance Matrix UPGMA begins with a distance matrix, which contains the pairwise distances between all sequences being compared. These distances can be based on sequence alignment, protein structure comparisons, or other relevant metrics. \[D_{i,j}=\max\begin{cases}D_{i-1,j-1} & + & s(a_i,b_j) \\D_{i-1,j} & + & s(a_i,-) \\D_{i,j-1} & + & s(-,b_j)\end{cases}=\max\begin{cases}D_{i-1,j-1}& + ...
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Predicting Functional Regions in the Protein Sequence using SMART

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Prediction of functional regions in the protein sequence plays a crucial role in the computer-aided drug discovery. SMART (a Simple Modular Architecture Research Tool) helps identify and annotate protein domains and analyze domain architectures by BLAST search. In bioinformatics, domains refer to distinct functional, structural, or evolutionary units within proteins, DNA, or RNA. Here are some key types of domains in bioinformatics: 1. Protein Domains Structural Domains : Compact, independently folding units within a protein (e.g., SH3, zinc finger, immunoglobulin domains). Functional Domains : Regions responsible for specific biochemical activities (e.g., kinase domain, DNA-binding domain). Evolutionary Domains : Conserved regions indicating common ancestry (e.g., Pfam domains). 2. DNA/RNA Domains Regulatory Domains : DNA regions controlling gene expression (e.g., promoters, enhancers). Functional RNA Domains : Motifs in non-coding RNAs (e.g., ribozyme catalytic cor...
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YouTube Video ID Grabber - Works for both video and shorts

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This page is designed to extract the video ID from a YouTube video URL. I have used a simple JavaScript regular expression to match the pattern and extract the video ID from the string. The JavaScript regular expression code is provided below, /[?=/]([A-Za-z0-9_-]{10}[AEIMQUYcgkosw048])[?=/]*?/g Live demonstration: YouTube Video ID Grabber Enter the YouTube URL Regular Expression Explanation [ Character set. Match any character in the set. ? Character. Matches a "?" character (char code 63). = Character. Matches a "=" character (char code 61). / Character. Matches a "/" character (char code 47). ] ( Capturing group #1. Groups multiple tokens together and creates a capture grou...
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Isaac Newton's Apple Falling Animation Effect using Google and Chrome DevTools

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Google has released an amazing animation effect that appears when you click on the apple on the page that appears when you search for " Isaac Newton " or " Sakura ." This is my simple try with a tiny JavaScript to create additional effects, like more apples falling automatically without clicking on the apple image. The effect appears on the screen as a live wallpaper. The JavaScript code used in the video tutorial is bellow, setInterval(function() { document.getElementsByClassName("smm4bb")[0].click(); }, 100); Note: To paste code into the terminal, enter "allow pasting" when requested. If you don't put "allow pasting," nothing will happen and no code will be pasted. The warning won't appear again after pasting permission has been granted.
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