State of the art: refinement of multiple sequence alignments

  • Saikat Chakrabarti1Email author,

    Affiliated with

    • Christopher J Lanczycki1,

      Affiliated with

      • Anna R Panchenko1,

        Affiliated with

        • Teresa M Przytycka1,

          Affiliated with

          • Paul A Thiessen1 and

            Affiliated with

            • Stephen H Bryant1

              Affiliated with

              BMC Bioinformatics201011:3

              DOI: 10.1186/1471-2105-11-3

              Received: 10 November 2009

              Accepted: 4 January 2010

              Published: 4 January 2010

              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

              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.PubMedView Article

              Copyright

              © Chakrabarti et al. 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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