Bowtie: Burrows Wheeler Transform

[Siva]

I have used Bowtie to align maize short sequence reads. I have a rather naive question regarding the application of the underlying algorithm. I just thought I would pose it here. How is the Burrows Wheeler Transform algorithm used in in the multiple alignment/short sequence alignment? Does the genome "index" building (Bowtie Index) also use this algorithm? Any details greatly appreciated.

Siva

[mgogol]

Here's a powerpoint presentation I made for our journal club where I attempt to explain the burroughs wheeler transform algorithm...

I think you are doing the burroughs wheeler transformation when you create the genome index, and then the alignment part is just doing a lookup into that transformed genome.

If anybody else looks at this presentation and finds I have it wrong, please correct me!

[Siva]

Hi mgogol
Thanks a lot. I will go through your ppt presentation and get back to you.

Siva

[lh3]

If I were asked to explain how BWT works in sequence alignment in one sentence, I would say BWT effectively mimics suffix tree but with much smaller memory footprint. About how it mimics you need to understand backward search/LF mapping, which will take some time to understand and even more time to prove.