Paper Info
Title
Comparing DNA sequence collections by direct comparison of compressed text indexes
Abstract
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 http://beetl.github.com/BEETL/ as part of the BEETL library.
Year
DOI
Venue
2012
10.1007/978-3-642-33122-0_17
WABI
Keywords
Field
DocType
indexing data structure,text index,direct comparison,query sequence,external memory,popular sequence alignment tool,beetl library,all-against-all comparison,dna sequence collection,individual query sequence,burrows-wheeler transform,sequence collection,large genomic data set
Sequence alignment,Data mining,Data structure,Data set,Computer science,Search engine indexing,DNA sequencing,Bioinformatics,Reference genome,Auxiliary memory
Conference
ISSN
Citations 
PageRank 
Lecture Notes in Computer Science Volume 7534, 2012, pp 214-224
10
0.59
References 
Authors
12
4
Name
Order
Citations
PageRank
Anthony J Cox119813.63
Tobias Jakobi2755.22
Giovanna Rosone319321.77
Ole B Schulz-Trieglaff426323.38