Apa Itu Metagenomik? Bedanya Amplicon dan Shotgun, serta Contohnya di Dunia Pertanian Organik

Pendahuluan: Apa itu Metagenomik?

Metagenomik secara umum adalah studi tentang seluruh materi genetik yang ditemukan dalam suatu komunitas mikroba di lingkungan tertentu, tanpa harus melakukan isolasi dan kultur mikroorganisme satu-per-satu.

Dengan kata lain, daripada menumbuhkan bakteri di cawan dan kemudian meng­urutkan genomnya, kita melakukan ekstraksi DNA atau RNA dari seluruh komunitas mikroba (misalnya tanah, air, daun tumbuhan, usus) dan kemudian melakukan sequencing untuk mengetahui “siapa hadir” dan/atau “apa yang bisa dilakukan (fungsi)” oleh komunitas tersebut.

Metagenomik memungkinkan kita menggali ekosistem mikroba yang sebelumnya sulit atau tidak bisa dikultur — dan membuka peluang besar dalam berbagai bidang seperti ekologi mikroba, agrikultur, bioteknologi, kedokteran, lingkungan.

Namun, dalam praktiknya ada beberapa pendekatan berbeda — dua yang paling umum adalah amplicon metagenomics dan shotgun metagenomics. Kedua pendekatan ini memiliki kelebihan dan kelemahan, serta cocok untuk jenis pertanyaan riset yang berbeda.

Sejarah DNA Sekuensing

Pendahuluan

DNA (asam deoksiribonukleat) adalah molekul genetik yang menyimpan informasi biologis dari makhluk hidup. Mengetahui secara tepat urutan basa DNA (A, T, G, C) sangat penting dalam genetika, biologi molekuler, evolusi, diagnosis penyakit, penelitian genomik, dan aplikasi bioteknologi lainnya. Namun, proses penentuan urutan DNA (sekuensing) tidaklah mudah: metode‐metode awal sangat lambat, labor intensif, dan mahal. Seiring waktu, teknologi berkembang dari metode generasi pertama (low throughput) ke generasi kedua (high throughput, pendek) dan generasi ketiga (single molecule, long reads). Artikel ini menelusuri perjalanan teknologi tersebut.

Awal Mula: Menjelajah DNA sebelum “sekuensing modern”

Sebelum teknologi sekuensing modern muncul, para peneliti mempelajari sifat kimia DNA, memisahkan untai, dan memetakan fragmen berdasarkan teknik kimia dan fisika. Namun penentuan urutan basa secara langsung belum mungkin.

What Is Next-Generation Sequencing (NGS) and Why It Matters in Modern Science

 Introduction

In the past, sequencing a single human genome could take years and cost millions of dollars. Today, thanks to Next-Generation Sequencing (NGS), scientists can decode entire genomes within hours at a fraction of the cost. This powerful technology has transformed biology, medicine, agriculture, and even environmental research.

What Is NGS?

Next-Generation Sequencing (NGS) refers to advanced DNA sequencing technologies that allow millions of DNA fragments to be read simultaneously. Unlike traditional Sanger sequencing, which processes one fragment at a time, NGS performs massively parallel sequencing, producing huge amounts of data quickly and accurately.

How Does NGS Work?

Understanding the Basics of Molecular Docking

 

Understanding the Basics of Molecular Docking

Molecular docking is a computational technique used to predict how a small molecule (ligand) interacts with a larger biological target such as a protein, enzyme, or nucleic acid. It plays a crucial role in drug discovery, allowing scientists to explore how potential drug candidates might bind to their target receptors and exert biological effects.

1. What Is Molecular Docking?

Molecular docking simulates the interaction between two molecules to predict the most stable binding pose and estimate the binding affinity. The process involves two main components:

• Receptor (Target): The biological molecule, typically a protein, responsible for a physiological function.

• Ligand: A small molecule that can bind to the receptor to modulate its activity.

The docking algorithm searches for the optimal orientation of the ligand within the receptor's binding site and scores each possible configuration based on the predicted strength of interaction.

 

🔬 Exploring NCBI BLAST: The Engine Behind Modern Bioinformatics

Have you ever wondered how scientists compare DNA or protein sequences across thousands of organisms in seconds? Welcome to NCBI BLAST — one of the most powerful and widely used bioinformatics tools in the world.

🧠 What Is NCBI BLAST?

BLAST stands for Basic Local Alignment Search Tool. It’s an algorithm developed by the National Center for Biotechnology Information (NCBI) to compare biological sequences such as DNA, RNA, or proteins against a massive database of known sequences.

Overview of Popular Bioinformatics Databases: Unveiling the Treasures of Genomic Knowledge

 

Introduction

Bioinformatics databases have become indispensable tools in genomics research, enabling scientists to manage, analyze, and explore the vast amount of genomic data generated by high-throughput sequencing technologies. These databases serve as virtual storehouses of genomic information, offering researchers access to curated data, analysis tools, and annotation resources. In this article, I will provide an overview of some of the most popular bioinformatics databases, highlighting their key features, applications, and contributions to genomic research. By unveiling the treasures of genomic knowledge hidden within these databases, I aim to empower researchers and enthusiasts in pursuing scientific discoveries. 

Bioinformatics: A Comprehensive Introduction to the Power of Data in Biology

In the era of big data and scientific advancements, biology has become increasingly reliant on computational tools and techniques to make sense of the vast amount of information generated. This interdisciplinary field, known as bioinformatics, combines biology, computer science, statistics, and data analysis to gather, organize, and interpret biological data. 

Bioinformatics has revolutionized the way we study and understand living organisms, from unraveling the complexities of the human genome to predicting the structure and function of proteins. In this article, we will provide a comprehensive introduction to bioinformatics and explore its importance in modern biological research.