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Table 4 Correct alignments using gapmis, gapmis_one_to_one_f, gapmis_one_to_one_onf, and needle.

From: libgapmis: extending short-read alignments

Species

Length of queries [bp]

Gap occurrence frequency

gapmis

gm -f 2

gm -f 3

gm -onf 2

gm -onf 3

needle

AT

100

2.4 × 10-5

999,099

998,404

997,561

999,207

999,259

999,126

AT

150

2.4 × 10-5

998,805

998,171

997,542

999,024

999,152

999,115

BV

100

1.7 × 10-5

999,361

998,868

998,229

999,432

999,459

999,353

BV

150

1.7 × 10-5

999,196

998,771

998,249

999,347

999,432

999,378

HS

100

5.7 × 10-6

999,809

999,615

999,419

999,822

999,825

999,782

HS

150

5.7 × 10-6

999,795

999,606

999,408

999,817

999,825

999,793

  1. The correct alignments of 1, 000, 000 pairs of simulated sequences with various observed gap occurrence frequencies using gapmis, gapmis_one_to_one_f, gapmis_one_to_one_onf, and needle. Each of the datasets consists of 1,000,000 pairs of sequences; the highest number of correct alignments for each dataset is shown in bold.