SUPPLEMENTAL MATERIAL

HTML tables or pages | Documents | Description |
---|---|---|

Align Training set | Word (.doc) Acrobat (.pdf) tar-gziped (.tar.gz) |
Training set of pairwise alignments for sequence alignment (word table) (raw data) |

Align Testing set | Word (.doc) Acrobat (.pdf) tar-gziped (.tar.gz) |
Testing set of pairwise alignments for sequence alignment |

Good/Bad models | --- | Sets of correct and incorrect three-dimensional models (comparative models) |

Statistical Potentials | --- | Statistical potentials based on the reduced amino acid alphabets |

Similarity matrices | --- | Reduced similarity matrices for sequence alignment |

Random Alphabets | --- | Description of random alphabets (5 types each) Optimal gap opening and extension penalties of reduced similarity matrices based on these alphabets |

Reduced Alphabets | --- | Optimal reduced amino acid alphabets generated by the genetic algorithm |