Construct a semi-global alignment

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Reference no: EM13501404

Bioinformatic assignment, This is a code in Ruby language. This code is to do a global alignment, and needs to be in semi-global alignment.

Modify the code of global alignment to be semi-global alignment.

What changes are needed to construct a semi-global alignment. The global alignment works pretty well on sequences that are nearly the same length. Let's try another example where the sequence lengths are more disparate.• $ ruby global.rb -d cgctatag cta

• Dynamic programming table:

• | | c | g | c | t | a | t | a | g |

• ----+------+------+------+------+------+------+------+------+------+

• | | | | | | | | | |

• | 0 |< -1 |< -2 |< -3 |< -4 |< -5 |< -6 |< -7 |< -8 |

• ----+------+------+------+------+------+------+------+------+------+

• | ^ |\ | |\ | | | | | |

• c | -1 | 1 |< 0 |< -1 |< -2 |< -3 |< -4 |< -5 |< -6 |

• ----+------+------+------+------+------+------+------+------+------+

• | ^ | ^ |\ |\ |\ | |\ | | |

• t | -2 | 0 | 1 |< 0 | 0 |< -1 |< -2 |< -3 |< -4 |

• ----+------+------+------+------+------+------+------+------+------+

• | ^ | ^ |\ ^ |\ |\ |\ | |\ | |

• a | -3 | -1 | 0 | 1 |< 0 | 1 |< 0 |< -1 |< -2 |

• ----+------+------+------+------+------+------+------+------+------+

• Alignment 1

• cgctatag

• __c__ta_

• Alignment 2

• cgctatag

• c____ta_

• Alignment 3

• cgctatag

• __ct__a_

• Alignment 4

• cgctatag

• c__t__a_

• Alignment 5

• cgctatag

• __cta___

• Alignment 6

• cgctatag

• c__ta___

Reference no: EM13501404

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