Skip to main content

Table 5 Comparing AWFM and SeqAn3 Locate() performance for amino acid search, across various suffix array compression ratios

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

Compression ratio

Amino acid locate()—200Mb

Time (s)

Peak memory (Mb)

SeqAn3

AWFM

SeqAn3

AWFM

1

3.30

0.83

822

1003

2

7.05

2.60

481

661

4

15.37

6.21

310

490

8

34.33

12.95

224

405

16

79.01

27.49

182

362

  1. The target sequence is a 200 million-character long amino acid sequence generated by the easel tool ‘esl-shuffle’. Query consists of 1 million amino acid queries of length 6 taken from the target sequence. Default k-mer lookup table size of 5 was used. Time and peak memory were captured with /usr/bin/time
Back to article page

Algorithms for Molecular Biology

ISSN: 1748-7188