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BioJulia / BioAlignments.jl

Sequence alignment tools
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Bug in `OverlapAlignment` #59

Closed jakobnissen closed 2 years ago

jakobnissen commented 2 years ago

Align these two sequences

a = AGTAAAGATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATATGCTTCTTCATGCAAATTGCCATCCTGATAACTACTGTAACATTGCATTTCAAGCAATATGAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGAAACATAACAGAGATAGTGTATTTGACCAACACCACCATAGAGAGGGAAATATGCCCCAAACCAGCAGAATACAGAAATTGGTCAAAACCGCAATGTGGCATTACAGGATTTGCACCTTTCTCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCTTATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACAATAAACAACGTGCATTCAAATAACACAGCACGTGATAGGACCCCTCATCGGACTCTATTGATGAATGAGTTGGGTGTTCCTTTCCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGCTCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAATGCAACTGCTAGTTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAAGATATTCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTAATGACTGATGGAAATGCTACAGGAAAAGCTGATACTAAAATATTATTCATTGAGGAGGGGAAAATCGTTCATACTAGCAAATTGTCAGGAAGTGCTCAGCATGTCGAAGAGTGCTCTTGCTATCCTCGATACCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGATCCAACCGGCCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGACTTGTTGGAGACACACCCAGAAAAACCGACAGCTCCAGCAGCAGCCATTGCTTGAATCCTAACAATGAAAAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTGTGGATGGGGAGAACAATCAACGAGACGTCACGCTTAGGGTATGAAACCTTCAAAGTCGTTGAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGAGGTGATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGGTGCTTTTATGTGGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCAAACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGATGGGGCGGACCTCAATCTCATGCATATATAAGCTTTCGCAATTTTAGAAAAAACT

b = ACTGAGGCAAATAGGCCAAAAATGAACAATGCTACCTTCAACTATACAAACGTTAACCCTATTTCTCACATCAGGGGGAGTGTTATTATCACTATATGTGTCAGCTTCATTGTCATACTTACTATATTCGGATATATTGCTAAAATTTTCACAAACAGAAATAACTGCACCAATAATGCCATTGGATTGTGCAAACGCATCAAATGTTCAGGCTGTGAACCGTTCTGCAACAAAAGGGGTGACACTTCTTCTCCCAGAACCGGAGTGGACGTATCCTCGTTTATCTTGCCCGGGCTCAACCTTTCAGAAAGCACTCCTAATTAGCCCCCATAGATTCGGAGAAACCAAAGGAAACTCAGCTCCCTTGATAATAAGGGAACCTTTTATTGCTTGTGGACCAAAGGAATGCAAACACTTTGCTCTAACCCATTATGCAGCTCAGCCAGGGGGATACTACAATGGAACAAGAGAAGACAGAAACAAGCTGAGGCATCTAATTTCAGTCAAATTGGGCAAAATCCCAACAGTAGAAAACTCTATTTTCCACATGGCAGCTTGGAGCGGGTCCGCATGCCATGATGGTAGAGAATGGACATACATCGGAGTTGATGGCCCCGACAGTAATGCATTGCTCAAAATAAAATATGGAGAAGCATATACTGACACATACCATTCCTATGCAAAAAACATCCTAAGGACACAAGAAAGTGCCTGCAATTGCATCGGGGGAGATTGTTATCTTATGATAACTGATGGCCCAGCTTCAGGGATTAGTGAATGCAGATTCCTTAAGATTCGAGAGGGCCGAATAATAAAAGAAATATTTCCAACAGGAAGAGTAAAACATACTGAGGAATGCACATGCGGATTTGCCAGCAACAAAACCATAGAATGTGCCTGTAGAGATAACAATTACACAGCAAAAAGACCCTTTGTCAAATTAAATGTGGAGACTGATACAGCGGAAATAAGATTGATGTGCACAGAGACTTATTTGGACACCCCCAGACCAAATGATGGAAGCATAACAGGGCCTTGCGAATCTAATGGGGACAAAGGGAGTGGAGGCATCAAAGGAGGATTTGTTCATCAAAGAATGGCATCCAAGATTGGAAGGTGGTACTCTCGAACGATGTCTAAAACTAAAAGAATGGGGATGGGACTGTATGTAAAGTATGATGGAGACCCATGGACTGATAGTGAAGCCCTTGCTCTTAGTGGAGTAATGGTTTCAATGGAAGAACCTGGTTGGTATTCCTTTGGCTTCGAAATAAAAGATAAGAAATGTGATGTCCCCTGTATTGGGATAGAAATGGTACATGATGGTGGGAAAACGACTTGGCACTCAGCAGCAACAGCCATTTACTGTTTAATGGGCTCAGGACAACTGCTGTGGGACACTGTCACAGGTGTTGATATGGCTCTGTAATGGAGGAATGGTTGAGTCTGTTCTAAACCCTTTGTTCCTATTTTGTTTGAACAATTGTCCTTACTGAACTTAATTGTTTCTGAA

With the following code

pairalign(OverlapAlignment(), a, b, AffineGapScoreModel(EDNAFULL, gap_open=-25, gap_extend=-2))

The resulting alignment only aligns part of a, and is therefore not a global-global alignment.

jakobnissen commented 2 years ago

Once again, I can't read an alignment. There is no bug.