Open Access

Erratum to: OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations

BMC Genomics201718:488

https://doi.org/10.1186/s12864-017-3849-5

Received: 7 June 2017

Accepted: 7 June 2017

Published: 27 June 2017

The original article was published in BMC Genomics 2017 18:390

Erratum

After publication of the original article [1] the authors found the following errors had occurred:
  1. 1.

    Saccaromyces should be spelt Saccharomyces in Table 1. (Table 1)

     
  2. 2.

    Kluveromyces should be spelt Kluyveromyces in Table 1. (Table 1)

     
  3. 3.

    Table 4, columns 3, 5, 7 and 9: All values within these columns should be placed in brackets to indicate the standard deviation. (Table 4)

     
  4. 4.

    The legend for Table 4 should read: ‘Numbers shown are rounded mean values from 5 disjoint removed subsets of genes, with standard deviations bracketed and not ‘10 removed subsets’ as per the original article. (Table 4)

     
Table 1

Species Set A, fungal species used for algorithm validation

Species Name

Source

Strain

Taxonomy ID

References

Eremothecium gossypii

JGIa

ATCC10895

284,811

[12]

Debaromyces hansenii

JGI

CBS767

284,592

[13] [14]

Kluyveromyces lactis

JGI

CLIB210

284,590

[13]

Saccharomyces cerevisiae

SGDb

S288C

559,292

[24]

Yarrowia lipolytica

JGI

CLIB122

284,591

[13]

aJoint Genome Institute; bSaccharomyces Genome Database

Table 4

Recovery of removed genes in A. thaliana, averaged over five runs

 

10% annotations removed

90% annotations removed

OrthoFiller

de novo

OrthoFiller

de novo

No. genes removed

2410

2410

21,683

21,683

Total genes founda

1233

(37.5)

13,184

(426.7)

11,480

(96.2)

42,504

(223.5)

Found genes which overlap removed genesa

1106

(37.5)

4918

(130.4)

11,343

(89.0)

35,609

(149.5)

Total recovered genesa

1035

(31.72)

2268

(16.4)

10,380

(59.7)

20,430

(33.0)

Number of split genesa

67

(5.4)

1213

(23.6)

944

(34.4)

7451

(37.7)

Mean pF-score of found genesa

0.75

(0.01)

0.45

(<0.01)

0.70

(<0.01)

0.55

(<0.01)

Mean oF-score of found genesa

0.94

(<0.01)

0.51

(<0.01)

0.89

(<0.01)

0.64

(<0.01)

High-quality found genes (pF-score ≥ 0.95)a

432.0

(29.3)

640.8

(27.4)

3419.8

(21.3)

9079.6

(99.5)

Lower-quality found genes (pF-score < 0.95)a

674.6

(32.1)

4277.2

(147.8)

7923.8

(99.5)

26,529.8

(201.3)

Mean pF-score of lower-quality genesa

0.61

(0.02)

0.31

(<0.01)

0.57

(<0.01)

0.33

(<0.01)

% of lower-quality genes with oF-score < 0.95a

34.6

(1.9)

81.1

(0.9)

43.4

(0.6)

73.9

(0.1)

aNumbers shown are rounded mean values from 5 disjoint removed subsets of genes, with standard deviations bracketed

The original article has been corrected.

Corrected versions of all figures and tables are included in this Erratum:

Corrected Table 1

Corrected Table 4

Notes

Declarations

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Authors’ Affiliations

(1)
Department of Plant Sciences, University of Oxford

Reference

  1. Dunne M, Kelly S. OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations. BMC Genomics. 2017;18:390. doi:10.1186/s12864-017-3771-x.View ArticlePubMedPubMed CentralGoogle Scholar

Copyright

© The Author(s). 2017

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