Sentence examples for using a suffix array from inspiring English sources

This step can be done in linear time using a suffix array data structure [ 34].

Using a suffix array based clustering approach, we have identified 25,971 clusters and 40,877 singleton sequences.

We used the method of Baeza-Yates and Perleberg [ 26] to match reads up to 2-edits, the same method used by Illumina's own aligner Eland. 1. Index the genome using a suffix array.

Using a suffix array, exact string queries can be answered in O(m log n) time, where m is the length of the query, instead of O(m+ n) time without a suffix array.

Oligomers of all lengths can be indexed using a suffix array or its compressed BWT equivalent, as used in Bowtie, BWA and SOAP2, which can represent a reference sequence compactly, in 2 GB for a human-sized genome of 3 billion nt.

It uses a suffix array index to map reads onto a reference genome.

DNACLUST [ 40] also follows greedy incremental approach; it uses a suffix array to index the input data set.

However, because RAPSearch uses a suffix array to index the database sequences for seed identification, it uses substantial memory for searches in large databases.

A notable exception is the Edena assembler (Hernandez et al., 2008) that uses a suffix array to compute exact overlaps between reads that are then used to construct the string graph.

Over the course of time, several approaches have been used: Blast uses a finite state machine from all 'related' query k-mers, Bowtie searches its seeds in an FM-Index, RAPSearch uses a suffix array to find seeds, RAPSearch2 and UBlast use hash-tables.

The reads were then mapped to the genome using a suffix-array-based approach.