The construction of suffix trees for very long sequences is essential for many applications, and it plays a central role in the bioinformatic domain. With the advent of modern sequencing technologies, biological sequence databases have grown dramatically. Also the methodologies required to analyze these data have become more complex everyday, requiring fast queries to multiple genomes. In this article, we present parallel continuous flow (PCF), a parallel suffix tree construction method that is suitable for very long genomes. We tested our method for the suffix tree construction of the entire human genome, about 3GB. We showed that PCF can scale gracefully as the size of the input genome grows. Our method can work with an efficiency of 90% with 36 processors and 55% with 172 processors. We can index the human genome in 7 minutes using 172 processes.

/pdf/parallel-continuous-flow-a-parallel-suffix-tree-construction-3ocnq5llrt.pdf

Parallel continuous flow: a parallel suffix tree construction tool for whole genomes.

Dynamic suffix array is a suffix data structure that reflects various patterns in a mutable string Dynamic suffix array is rather convenient for performing substring search queries over database indexes that are frequently modified We are to introduce an O(nlog2n) algorithm that builds suffix array for any string and to show how to implement dynamic suffix array using this algorithm under certain constraints We propose that this algorithm could be useful in real-life database applications

/pdf/simple-algorithm-to-maintain-dynamic-suffix-array-for-text-4qoxhzndkz.pdf

Simple Algorithm to Maintain Dynamic Suffix Array for Text Indexes

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Simple Algorithm to Maintain Dynamic Suffix Array for Text Indexes