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Table 1 Comparative performance of GBParsy and other publicly available GBF parsers

From: GBParsy: A GenBank flatfile parser library with high speed

Source

A. thaliana

M. musculus

Accession

NC_003070

NT_039207

Sequence Length (Mbp)

30.4

116.4

File Size (MB)

59.0

144.0

GBParsy

0.9 ± 0.1 (1.0)

2.4 ± 0.3 (1.0)

GBParsyPy

1.7 ± 0.1 (1.8)

3.0 ± 0.5 (1.2)

EMBOSS

9.7 ± 0.2 (10.7)

12.7 ± 0.3 (5.3)

BioPerl

45.7 ± 0.4 (50.3)

38.7 ± 0.3 (16.0)

BioPython

109.2 ± 0.4 (120.3)

39.7 ± 0.2 (16.4)

  1. Elapsed time (sec) taken by each program was measured in 50 separate runs; mean ± standard deviation (SD) for these runs are shown. Average fold slowness in parenthesis is the ratio of each observed mean time to the one taken by the GBParsy test program.
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BMC Bioinformatics

ISSN: 1471-2105

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