Open Access

Erratum to: State of the art: refinement of multiple sequence alignments

  • Saikat Chakrabarti1Email author,
  • Christopher J Lanczycki1,
  • Anna R Panchenko1,
  • Teresa M Przytycka1,
  • Paul A Thiessen1 and
  • Stephen H Bryant1
BMC Bioinformatics201011:3

DOI: 10.1186/1471-2105-11-3

Received: 10 November 2009

Accepted: 4 January 2010

Published: 4 January 2010

The original article was published in BMC Bioinformatics 2006 7:499

Abstract

Correction to Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA and Bryant SH: State of the art: refinement of multiple sequence alignments. BMC Bioinformatics 2006, 7:499.

Correction

After publication of [1] we have noticed an error in our manuscript. We have realized that there were some numbers incorrectly inserted within the Table 1 of the manuscript [1]. Corrected values are now provided In Table 1, for six of the numbers that were entered incorrectly: the SP scores for References 1, 4 and 5 under Muscle reference alignment (REFINER refinement alignment) and, SP scores for References 2, 3 and 5 under T-Coffee reference alignment (Default refinement alignment). However, this does not affect our original interpretation of the data presented in our original publication in any way. We regret any inconvenience that this inaccuracy might have caused.
Table 1

Impact on alignment quality following refinement.

BAliBASE reference alignments

ClustalW

Dialign

Mafft

 

Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER

Reference 1

0.65

0.63

0.66

0.66

0.62

0.65

0.67

0.62

0.70

0.69

0.69

0.71

Reference 2

0.78

0.80

0.80

0.80

0.78

0.80

0.79

0.79

0.83

0.82

0.83

0.82

Reference 3

0.66

0.69

0.67

0.68

0.65

0.64

0.65

0.66

0.76

0.73

0.75

0.77

Reference 4

0.67

0.68

0.66

0.70

0.67

0.71

0.66

0.69

0.75

0.73

0.70

0.77

Reference 5

0.65

0.67

0.66

0.68

0.67

0.65

0.64

0.67

0.76

0.73

0.72

0.76

Average

0.682

0.694

0.69

0.704

0.678

0.690

0.682

0.692

0.760

0.740

0.738

0.766

Increment (%)

0

1.760

1.173

3.226

0.000

1.770

0.590

2.065

0.000

-2.632

-2.895

0.789

BAliBASE reference alignments

Muscle

Probcons

T-Coffee

 

Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER

Default

RASCAL

RF

REFINER

Reference 1

0.66

0.66

0.67

0.68

0.72

0.72

0.70

0.73

0.68

0.68

0.69

0.68

Reference 2

0.80

0.81

0.80

0.80

0.83

0.83

0.82

0.82

0.8

0.83

0.82

0.82

Reference 3

0.71

0.71

0.71

0.73

0.76

0.73

0.75

0.77

0.61

0.62

0.62

0.64

Reference 4

0.71

0.72

0.68

0.74

0.77

0.75

0.71

0.77

0.71

0.71

0.70

0.72

Reference 5

0.70

0.71

0.67

0.72

0.76

0.74

0.71

0.75

0.72

0.73

0.69

0.74

Average

0.716

0.722

0.706

0.734

0.768

0.754

0.738

0.77

0.704

0.714

0.704

0.720

Increment (%)

0.000

0.838

-1.397

2.514

0.000

-1.823

-3.906

0.260

0.000

1.420

0.000

2.273

Notes

Authors’ Affiliations

(1)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health

References

  1. Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH: State of the art: refinement of multiple sequence alignments. BMC Bioinformatics 2006, 7: 499. 10.1186/1471-2105-7-499View ArticlePubMedPubMed CentralGoogle Scholar

Copyright

© Chakrabarti et al; licensee BioMed Central Ltd. 2010

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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