Why the genome/transcriptome will be indexed before mapping

Question

[seta]

Hi all,

As far as I know, at the first, the genome / transcriptome will be indexed by the related software for mapping, and then mapping will be done. Could you please explain to me what is the concept of indexing and why it should be done? Sorry if you find this question is a dumb one.

Thanks in advance

[h.mon]

It is similar to the index of a book: it allows fast searches on reduced or compressed, yet useful, information. I like this intro for a friendly introduction on Burrows-Wheeler Transform and FM Index, two common techniques used in bioinformatics.

Answer 1

[mastal511]

It helps the mapping algorithms to work faster. Indexing is like creating a dictionary of where in the genome to find a particular sequence.

Answer 2

[ATpoint]

If you want details, refer to Ben Langmeads (developer of the bowtie aligners) youtube channel, where he lectures about concepts of sequence alignments, including the purpose and concept of indexing:

https://www.youtube.com/channel/UCrDmN9uRVJR7KM8aRE_58Zw