# Read alignment: exact matching

Read alignment, also known as sequence alignment, refers to the process of mapping or aligning short sequence reads obtained from high-throughput sequencing technologies to a reference genome or transcriptome. The goal is to determine where each read likely originated from in the reference sequence. This information is important for many downstream applications, such as variant calling, i.e. identifying differences between the reads and the reference genome,  and transcriptome analysis, i.e. identifying which genes are being transcribed and at what levels.

There are numerous algorithms designed for aligning reads to a genome. This section introduces fundamental exact matching algorithms, which specifically locate exact occurrences of a given string of characters within a larger body of text or identify patterns in text.

### Read alignment and why it's hard

{% embed url="<https://www.youtube.com/watch?v=PMGstYcBgTY&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=15>" %}

### Naive exact matching

{% embed url="<https://www.youtube.com/watch?v=KUbsdGm3G7s&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=16>" %}

### Practical: Matching artificial reads

{% embed url="<https://www.youtube.com/watch?v=ep91JWd6fs0&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=17>" %}

### Practical: Matching real reads

{% embed url="<https://www.youtube.com/watch?v=SFYpw87lHWQ&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=18>" %} <br>
{% endembed %}

### Boyer-Moore basics

{% embed url="<https://www.youtube.com/watch?v=4Xyhb72LCX4&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=19>" %}

### Boyer-Moore: putting it all together

{% embed url="<https://www.youtube.com/watch?v=Wj606N0IAsw&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=20>" %}

### Diversion: Repetitive elements

{% embed url="<https://www.youtube.com/watch?v=ZwHCRb_y7vA&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=21>" %}

### Practical: Implementing Boyer-Moore

{% embed url="<https://www.youtube.com/watch?v=CT1lQN73UMs&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=22>" %}

## Problems to solve

Try to solve these problems after completing the section.\
Some of them may be challenging :)

1. [Finding a Motif in DNA](https://rosalind.info/problems/subs/)
2. [Open Reading Frames](https://rosalind.info/problems/orf/)
3. [RNA Splicing](https://rosalind.info/problems/splc/)

## 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.