> For the complete documentation index, see [llms.txt](https://edu.abi.am/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://edu.abi.am/bioinformatics-algorithms/indexing-before-alignment.md).

# Indexing before alignment

Indexing is an essential step in many bioinformatics applications, as it can greatly reduce the computational time and resources required for sequence alignment. It allows the alignment algorithm to quickly locate the query sequences in the reference genome, without having to search the entire genome for matches. In this section you will learn how indexing works.<br>

### Preprocessing

{% embed url="<https://www.youtube.com/watch?v=HGVQi5xX44M&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=23>" %}

### Indexing and k-mer indexes

{% embed url="<https://www.youtube.com/watch?v=2UsmUgJtwAI&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=24>" %}

### Ordered structures for indexing

{% embed url="<https://www.youtube.com/watch?v=CA0_CxKe_SY&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=25>" %}

### Hash tables for indexing

{% embed url="<https://www.youtube.com/watch?v=X2OTyGTi82M&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=26>" %}

### Practical: Implementing a k-mer index

{% embed url="<https://www.youtube.com/watch?v=LUcAXi2TijM&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=27>" %}

### Variations on k-mer indexes

{% embed url="<https://www.youtube.com/watch?v=My_sw_Rf_4U&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=28>" %}

### Genome indexes used in research

{% embed url="<https://www.youtube.com/watch?v=bfnFgcB_Nlw&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA&index=29>" %}

## Problem to solve

Try to solve this problem after completing the section.

1. [Finding a Spliced Motif](https://rosalind.info/problems/sseq/)

## 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.


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