Abstract
We investigate the problem of building a suffix array substring index for inputs significantly larger than main memory. This problem is especially important in the context of biological sequence analysis, where biological polymers can be thought of as very large contiguous strings. The objective is to index every substring of these long strings to facilitate efficient queries. We propose a new simple, scalable, and inherently parallelizable algorithm for building a suffix array for out-of-core strings. Our new algorithm, Suffix Rank , scales to arbitrarily large inputs, using disk as a memory extension. It solves the problem in just O (log n ) scans over the disk-resident data. We evaluate the practical performance of our new algorithm, and show that for inputs significantly larger than the available amount of RAM, it scales better than other state-of-the-art solutions, such as eSAIS, SAscan , and eGSA.
Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
