# DNA strings and sequencing file formats

In this section, you will follow a few videos to revise your knowledge about the nature of DNA strings, the basics of working with genomes and reads, and the different file formats. After you're done with the videos, you will find a few problems to solve and check your knowledge and programming skills. The practical videos are explained in Python, but feel free to use any language of your choice to reproduce the same algorithm.

## DNA strings and sequencing

### Why study DNA sequencing and computational genomics?

{% embed url="<https://www.youtube.com/watch?v=hpb-mH-yjLc&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=1>" %}

### DNA: the molecule, the string

{% embed url="<https://www.youtube.com/watch?v=s1j-DuYJFr0&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=3>" %}

### String definitions and Python syntax

{% embed url="<https://www.youtube.com/watch?v=xmFR9VXzG7c&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=4>" %}

### Practical: String basics

{% embed url="<https://www.youtube.com/watch?v=YA2lBLz40SM&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=5>" %}

### Practical: Manipulating DNA strings

{% embed url="<https://www.youtube.com/watch?v=DphFe1vFJmU&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=6>" %}

### Practical: Downloading and reading a genome

{% embed url="<https://www.youtube.com/watch?v=FEvaKOZDDBk&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=7>" %}

### How DNA is copied

{% embed url="<https://www.youtube.com/watch?v=vaYxqrKn7Pk&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=8>" %}

### Sequencing by Synthesis

{% embed url="<https://www.youtube.com/watch?v=IzXQVwWYFv4&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=9>" %}

### Base calling and sequencing errors

{% embed url="<https://www.youtube.com/watch?v=U4QnpciIJhM&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=10>" %}

## File formats to store DNA reads

### Reads in FASTQ format

{% embed url="<https://www.youtube.com/watch?v=SZ6suqu-eLA&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=11>" %}

### Practical: Working with sequencing reads

{% embed url="<https://www.youtube.com/watch?v=YXVheiWAN5M&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=12>" %}

### Practical: Analyzing reads by position

{% embed url="<https://www.youtube.com/watch?v=7Nc04PFysEU&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=13>" %}

### Sequencers give pieces to genomic puzzles

{% embed url="<https://www.youtube.com/watch?v=X307VyAeHfI&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=14>" %}

## Problems to solve

To solve the following problems you need to [create an account on the Rosalind website](https://rosalind.info/accounts/register/) and [log in](https://rosalind.info/accounts/login/). On this site, you will find instructions on how to solve the problems and submit your answers. Please note that you need to solve the problems in the specified order. The problems will open up for you to solve only after you have unlocked the previous problems.&#x20;

Now, try to solve these problems after completing all the videos above.\
Some of them may be challenging :)

1. [Counting DNA Nucleotides](https://rosalind.info/problems/dna/)
2. [Transcribing DNA into RNA](https://rosalind.info/problems/rna/)
3. [Complementing a Strand of DNA](https://rosalind.info/problems/revc/)
4. [Computing GC Content](https://rosalind.info/problems/gc/)
5. [Translating RNA into Protein](https://rosalind.info/problems/prot/)

## Congratulations!

If you made it here, then congratulations! You have successfully completed this section. Move to the next portion of the guide with the arrow buttons below.