6533b863fe1ef96bd12c78e6
RESEARCH PRODUCT
Comparing DNA sequence collections by direct comparison of compressed text indexes
Anthony J. CoxTobias JakobiGiovanna RosoneOle B. Schulz-trieglaffBen RaphaelJijun Tangsubject
Genomics (q-bio.GN)SequenceComputer sciencebusiness.industrySearch engine indexingSequence alignmentPattern recognitionConstruct (python library)Data structureBurrows-Wheeler Transform; Splice junctions; External memoryExternal memoryFOS: Biological sciencesCode (cryptography)Quantitative Biology - GenomicsBurrows-Wheeler TransformArtificial intelligencebusinessSplice junctionsAuxiliary memoryReference genomedescription
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 | journal | country | edition | language |
|---|---|---|---|---|
| 2012-01-01 |