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Table 4 Comparing AWFM and SeqAn3 Locate() performance for nucleotide search, across various suffix array compression ratios

From: An optimized FM-index library for nucleotide and amino acid search

Compression ratio

Nucleotide locate()—1Gb

Time (s)

Peak memory (Mb)

SeqAn3

AWFM

SeqAn3

AWFM

1

4.30

1.07

4007

4535

2

5.20

4.17

2176

2704

4

8.62

4.60

1261

1789

8

13.78

6.26

803

1331

16

24.48

11.90

574

1102

  1. The target sequence is a 1 billion-character long nucleotide sequence generated by the easel tool ‘esl-shuffle’. Query consists of 1 million nucleotide queries of length 14 taken from the target sequence. Default k-mer lookup table size of 12 was used. Time and peak memory were captured with /usr/bin/time
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Algorithms for Molecular Biology

ISSN: 1748-7188