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Pair HMM and the Stepping Stone algorithm

Pair HMM and the Stepping Stone algorithm. Mani Right Now. Our Pair HMM state diagram. Viterbi algorithm. Time complexity O( mns 2 ), Space complexity O( mns ) m – length of genomic sequence n – length of cDNA sequence s – number of states (~13 now)

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Pair HMM and the Stepping Stone algorithm

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  1. Pair HMM and the Stepping Stone algorithm Mani Right Now

  2. Our Pair HMM state diagram

  3. Viterbi algorithm • Time complexity O(mns2), Space complexity O(mns) • m – length of genomic sequence • n – length of cDNA sequence • s – number of states (~13 now) • Suffice to say that it could be a HUGE number!

  4. Viterbi Matrix Genomic sequence cDNA sequence

  5. Stepping stone – Seed Alignments Genomic sequence cDNA sequence

  6. Stepping Stone - Alignment Pins Genomic sequence cDNA sequence

  7. Viterbi Submatrices Savings: approx. 50% Genomic sequence cDNA sequence

  8. MGC test set • 10634 optimal alignments • 18000+ stepping stone alignments* • Compared the 10634 • Only 15 were different (0.14%!) * Still running

  9. Diff1 BC043644.12665. 474 TAGTAGAGGCGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCGAAATCCCG 523 |||||||| | ||||||| ||||||||| ||||||||||| ||| ||| | BC043644 1556 TAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTG 1605 BC043644.12665. 524 ACCTCAGGTGATCTGCCCACCTCAGCCTCCCAAAGTGCTGGGATT 568 ||||||||||||| ||||||| || ||||| |||||||||||| BC043644 1606 ACCTCAGGTGATCCACCCACCTGGGCTTCCCATAGTGCTGGGATT 1650 BC043644.12665. 474 TAGTAGAGGCGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCGAAATCCCG 523 |||||||| | ||||||| ||||||||| ||||||||||| ||| ||| | BC043644 1556 TAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTG 1605 BC043644.12665. 524 ACCTCAGGTGATCTGCCCA------------------------------- 542 ||||||||||||| |||| BC043644 1606 ACCTCAGGTGATCCACCCACCTGGGCTTCCCATAGTGCTGGGATTCAATT 1655 --//-- BC043644.12665. 543 ----------------------------------------------CCTC 546 |||| BC043644 3506 GTTGGCCAGGCTGGTCTCGAACTCCTGACATCAGGTGATCCACCTGCCTC 3555 BC043644.12665. 547 AGCCTCCCAAAGTGCTGGGATTAGAGGCGTGAACCAC 583 |||||||||||||||||||||| |||||||| |||| BC043644 3556 GGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC 3592

  10. Diff2 BC011727.13323. 18583 GGACTGATGAGGTCTTAACAAAAACCAGTGTGGCAAAAAAAAAAAAAAAA 18632 |||||||||||||||||||||||||||||||||||||||||||||||||| BC011727 1857 GGACTGATGAGGTCTTAACAAAAACCAGTGTGGCAAAAAAAAAAAAAAAA 1906 BC011727.13323. 18633 AAAAAAAAAAAAA 18645 ||||||||||||| BC011727 1907 AAAAAAAAAAAAA 1919 Score = 39 (77.8 bits), Expect = 0., Sum P(8) = 0., Group = 1 Identities = 39/39 (100%), Positives = 39/39 (100%), Strand = Plus / Plus Query: 1917 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATCCTAAAAAC 1955 ||||||||||||||||||||||||||||||||||||||| Sbjct: 18617 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATCCTAAAAAC 18655 BC011727.13323. 18583 GGACTGATGAGGTCTTAACAAAAACCAGTGTGGCAAAAAAAAAAAAAAAA 18632 |||||||||||||||||||||||||||||||||||||||||||||||||| BC011727 1857 GGACTGATGAGGTCTTAACAAAAACCAGTGTGGCAAAAAAAAAAAAAAAA 1906 BC011727.13323. 18633 AAAAAAAAAAAAATCCTAAAAACAAACAAACAAAAAAAA 18671 ||||||||||||| ||||| ||| ||| |||||||| BC011727 1907 AAAAAAAAAAAAA----AAAAAAAAAAAAAAAAAAAAAA 1941

  11. Diff3

  12. Diff3 – cont’d

  13. Placeholder Genomic sequence cDNA sequence

  14. Now what? • Compare with EST_GENOME • Null model • Use pairHMM for the ENCODE gene prediction workshop • Double pins

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