A statistical score for assessing the quality of multiple sequence alignments

doi:10.1186/1471-2105-7-484

BMC Bioinformatics

Volume 7

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Methodology article

A statistical score for assessing the quality of multiple sequence alignments

Virpi Ahola¹^,2 , Tero Aittokallio³^,6 , Mauno Vihinen⁴^,5 and Esa Uusipaikka²

¹Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland

²Department of Statistics, University of Turku, Turku, Finland

³Department of Mathematics, University of Turku, Turku, Finland

⁴Institute of Medical Technology, University of Tampere, Tampere, Finland

⁵Research Unit, Tampere University Hospital, Tampere, Finland

⁶Systems Biology Unit, Institut Pasteur, Paris, France

author email corresponding author email

BMC Bioinformatics 2006, 7:484doi:10.1186/1471-2105-7-484


Published:	3 November 2006

Additional files

Additional File 1:

MultiDisp visualization and conservation scores for the Ras-like protein positions 1–31. PNG formatted figure includes MultiDisp visualization of the Ras-like protein positions 1–31 (upper) and the corresponding conservation scores (lower). The curves show (red) the scaled -log(p)-values with Blosum62 scoring matrix, (magenta) the scaled -log(p)-values with grouping of amino acids, (blue) Mean Distance and (green) Information content scores for the alignment.

Format: PNG Size: 194KB Download file

Additional File 2:

MultiDisp visualization and conservation scores for the Ras-like protein positions 32–62. As 1, but for the Ras-like protein positions 32–62.

Format: PNG Size: 182KB Download file

Additional File 3:

MultiDisp visualization and conservation scores for the Ras-like protein positions 63–92. As 1, but for the Ras-like protein positions 63–92.

Format: PNG Size: 190KB Download file

Additional File 4:

MultiDisp visualization and conservation scores for the Ras-like protein positions 93–122. As 1, but for the Ras-like protein positions 93–122.

Format: PNG Size: 201KB Download file

Additional File 5:

MultiDisp visualization and conservation scores for the Ras-like protein positions 123–152. As 1, but for the Ras-like protein positions 123–152.

Format: PNG Size: 197KB Download file

Additional File 6:

MultiDisp visualization and conservation scores for the SH2 domain positions 1–27. PNG formatted figure includes MultiDisp visualization of the SH2 domain positions 1–27 (upper) and the corresponding conservation scores (lower). The curves show (red) the scaled -log(p)-values with Blosum62 scoring matrix, (magenta) the scaled -log(p)-values with grouping of amino acids, (blue) Mean Distance and (green) Information content scores for the alignment.

Format: PNG Size: 144KB Download file

Additional File 7:

MultiDisp visualization and conservation scores for the SH2 domain positions 28–55. As 6, but for SH2 domain positions 28–55.

Format: PNG Size: 170KB Download file

Additional File 8:

MultiDisp visualization and conservation scores for the SH2 domain positions 56–82. As 6, but for SH2 domain positions 56–82.

Format: PNG Size: 144KB Download file

Additional File 9:

MultiDisp visualization and conservation scores for the SH2 domain positions 83–109. As 6, but for SH2 domain positions 83–109.

Format: PNG Size: 144KB Download file

Additional File 10:

Tuning the importance sampling procedure. PDF file describes the simulation procedure for finding the appropriate parameter values of the importance sampling procedure.

Format: PDF Size: 42KB Download file

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