State of the art: refinement of multiple sequence alignments
Chakrabarti et al. BMC Bioinformatics 2010, 11:3
http://www.biomedcentral.com/1471-2105/11/3
CORRECTION
Open Access
State of the art: refinement of multiple
sequence alignments
Saikat Chakrabarti*, Christopher J Lanczycki, Anna R Panchenko, Teresa M Przytycka, Paul A Thiessen,
Stephen H Bryant
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
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
Reference 5
0.67
0.65
0.68
0.67
0.66
0.66
0.70
0.68
0.67
0.67
0.71
0.65
0.66
0.64
0.69
0.67
0.75
0.76
0.73
0.73
0.70
0.72
0.77
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
0
1.760
1.173
3.226
0.000
1.770
0.590
2.065
0.000
-2.632
-2.895
0.789
Increment
(%)
BAliBASE
reference
alignments
Muscle
Probcons
T-Coffee
Default
RASCAL
RF
REFINER
Default
RASCAL
RF
REFINER
Default
RASCAL
RF
REFINER
Reference 1
Reference 2
0.66
0.80
0.66
0.81
0.67
0.80
0.68
0.80
0.72
0.83
0.72
0.83
0.70
0.82
0.73
0.82
0.68
0.8
0.68
0.83
0.69
0.82
0.68
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
* Correspondence:
National Center for Biotechnology Information, National Library of Medicine,
National Institutes of Health, Bethesda, MD 20894, USA
© 2010 Chakrabarti et al; licensee 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.
Chakrabarti et al. BMC Bioinformatics 2010, 11:3
http://www.biomedcentral.com/1471-2105/11/3
Page 2 of 2
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.
Received: 10 November 2009
Accepted: 4 January 2010 Published: 4 January 2010
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.
doi:10.1186/1471-2105-11-3
Cite this article as: Chakrabarti et al.: State of the art: refinement of
multiple sequence alignments. BMC Bioinformatics 2010 11:3.
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