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Table 2 Overview of the presented algorithms

From: Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns

Algorithm

Online

Indexed

Early-stop

Additional memory

Used index tables

   

Acceleration

Requirements [bytes]

suf

lcp

suf −1

vtab

ScanAlign

✓

  

0

    

LScanAlign

✓

 

✓

0

    

LESAAlign

 

✓

✓

5n

✓

✓

  

LGSlinkAlign

 

✓

✓

9.125n

✓

✓

✓

✓

  1. The two online algorithms ScanAlign and LScanAlign need no additional memory except for the searched sequence of length n. Column additional memory requirements refers to the additional memory needed by the used index tables. Recall that tables suf and suf−1 require 4n bytes each. Table lcp can be stored in 1n bytes and the bit array vtab requires only n bits (= 0.125n bytes).