Bioinformatický seminár

Tue 9 Oct. 2012, 17:20

Title: Anthony J. Cox et al. Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes
Speaker: Martin Králik

Popular sequence alignment tools such as BWA convert a reference genome to 
an indexing data structure based on the Burrows-Wheeler Transform (BWT), 
from which matches to individual query sequences can be rapidly determined. 
However the utility of also indexing the query sequences themselves remains 
relatively unexplored.

Here we show that an all-against-all comparison of two sequence collections 
can be computed from the BWT of each collection with the BWTs held entirely 
in external memory, i.e. on disk and not in RAM. As an application of this 
technique, we show that BWTs of transcriptomic and genomic reads can be 
compared to obtain reference-free predictions of splice junctions that have 
high overlap with results from more standard reference-based methods.

Code to construct and compare the BWT of large genomic data sets is 
available at as part of the BEETL library.