Using Disco and MapReduce to study mRNA complexity Dan Williams - - PowerPoint PPT Presentation

7/14/2011 | Life Technologies Proprietary & Confidential |

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Using Disco and MapReduce to study mRNA complexity

Dan Williams

SciPy 2011 Lightning Talk

7/14/2011 | Life Technologies Proprietary & Confidential |

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Disco

• MapReduce framework written in Python

and Erlang

− useful for dealing with massive data

• Users specify map and reduce operations

as Python functions, then chain them together to get stuff done

7/14/2011 | Life Technologies Proprietary & Confidential |

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mRNA molecules contain three distinct regions:

AAATGACGACAACGGTGAGGGTTCTCGGGCGGGGCCTGGGACAGGCAGCTCCGGGGTCCGCGGTTTCACATCGGAAACAAAACAGCGG CTGGTCTGGAAGGAACCTGAGCTACGAGCCGCGGCGGCAGCGGGGCGGCGGGGAAGCGTATACCTAATCTGGGAGCCTGCAAGTGACA ACAGCCTTTGCGGTCCTTAGACAGCTTGGCCTGGAGGAGAACACATGAAAGAAAGAACCTCAAGAGGCTTTGTTTTCTGTGAAACAGT ATTTCTATACAGTTGCTCCAATGACAGAGTTACCTGCACCGTTGTCCTACTTCCAGAATGCACAGATGTCTGAGGACAACCACCTGAG CAATACTGTACGTAGCCAGAATGACAATAGAGAACGGCAGGAGCACAACGACAGACGGAGCCTTGGCCACCCTGAGCCATTATCTAAT GGACGACCCCAGGGTAACTCCCGGCAGGTGGTGGAGCAAGATGAGGAAGAAGATGAGGAGCTGACATTGAAATATGGCGCCAAGCATG TGATCATGCTCTTTGTCCCTGTGACTCTCTGCATGGTGGTGGTCGTGGCTACCATTAAGTCAGTCAGCTTTTATACCCGGAAGGATGG GCAGCTAATCTATACCCCATTCACAGAAGATACCGAGACTGTGGGCCAGAGAGCCCTGCACTCAATTCTGAATGCTGCCATCATGATC AGTGTCATTGTTGTCATGACTATCCTCCTGGTGGTTCTGTATAAATACAGGTGCTATAAGGTCATCCATGCCTGGCTTATTATATCAT CTCTATTGTTGCTGTTCTTTTTTTCATTCATTTACTTGGGGGAAGTGTTTAAAACCTATAACGTTGCTGTGGACTACATTACTGTTGC ACTCCTGATCTGGAATTTTGGTGTGGTGGGAATGATTTCCATTCACTGGAAAGGTCCACTTCGACTCCAGCAGGCATATCTCATTATG ATTAGTGCCCTCATGGCCCTGGTGTTTATCAAGTACCTCCCTGAATGGACTGCGTGGCTCATCTTGGCTGTGATTTCAGTATATGATT TAGTGGCTGTTTTGTGTCCGAAAGGTCCACTTCGTATGCTGGTTGAAACAGCTCAGGAGAGAAATGAAACGCTTTTTCCAGCTCTCAT TTACTCCTCAACAATGGTGTGGTTGGTGAATATGGCAGAAGGAGACCCGGAAGCTCAAAGGAGAGTATCCAAAAATTCCAAGTATAAT GCAGAAAGCACAGAAAGGGAGTCACAAGACACTGTTGCAGAGAATGATGATGGCGGGTTCAGTGAGGAATGGGAAGCCCAGAGGGACA GTCATCTAGGGCCTCATCGCTCTACACCTGAGTCACGAGCTGCTGTCCAGGAACTTTCCAGCAGTATCCTCGCTGGTGAAGACCCAGA GGAAAGGGGAGTAAAACTTGGATTGGGAGATTTCATTTTCTACAGTGTTCTGGTTGGTAAAGCCTCAGCAACAGCCAGTGGAGACTGG AACACAACCATAGCCTGTTTCGTAGCCATATTAATTGGTTTGTGCCTTACATTATTACTCCTTGCCATTTTCAAGAAAGCATTGCCAG CTCTTCCAATCTCCATCACCTTTGGG

Research question: Do the three mRNA regions generally differ in information content?

7/14/2011 | Life Technologies Proprietary & Confidential |

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Method: Calculate the Shannon entropy of each 21- nucleotide segment of each mRNA from a well-known

• database. Group results by region and compare.

MapReduce with Disco speeds the computation (across ~30k mRNA sequences)

7/14/2011 | Life Technologies Proprietary & Confidential |

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Map 21-mer segments and regions to 1 Reduce to remove duplicates Map Shannon entropy of 21-mer segment to region Reduce to get a boxplot for each region

7/14/2011 | Life Technologies Proprietary & Confidential |

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7/14/2011 | Life Technologies Proprietary & Confidential |

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Thank you!