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Cloudera, Inc.
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Hadoop World 2009 New York Oct 2, 2009 Sequence Alignment and Hadoop . Booz Allen Hamilton Inc. 134 National Business Parkway Annapolis Junction, MD 20701 Tel (301) 543-4665 [email_address] Paul Brown Associate
The Impact of Hadoop ,[object Object],[object Object],[object Object],[object Object]
Biological Information Paul Brown 9/21/09 Need to verify all these.
Biology + Computer Science = Bioinformatics http://bioinformatics.ubc.ca/about/what_is_bioinformatics A Y N A R N A N R N Y A Y N N R N A A N R N
Bioinformatics: The Pain ,[object Object],[object Object],[object Object],[object Object],Why Hadoop: ,[object Object],[object Object]
So What? Querying a database of sequences for similar sequences ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
So What? Comparing sequences in bulk ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Reconstructed Sequence
What if the dataset of sequences doesn't fit on one machine? ,[object Object],[object Object],Sequence: A B C D Pair: AB AC AD BC BD CD Input data Pre Joined Data MapReduce MapReduce Pre Join Data Alignment Results Alignment Algorithm 1 Alignment Algorithm 2 Alignment Algorithm N
So What? Analyzing really big sequences ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Demonstration Implementation: Smith-Waterman Alignment ,[object Object],[object Object],[object Object],[object Object]
Smith-Waterman Algorithm - A Y N A N A N A - 0 0 0 0 0 0 0 0 0 A 0 2 1 0 2 1 2 1 2 N 0 1 1 3 2 4 3 4 3 A 0 2 1 2 5 4 6 5 6 N 0 1 1 3 4 7 6 8 7 A 0 2 1 2 5 6 9 8 10 N 0 1 1 3 4 7 8 11 10 R 0 0 0 2 3 6 7 10 10 A 0 2 1 1 4 5 8 9 12
Hadoop and EC2 Implementation ,[object Object],[object Object],[object Object],[object Object]
Ready for What’s Next…. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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Hw09 Protein Alignment

  • 1. Hadoop World 2009 New York Oct 2, 2009 Sequence Alignment and Hadoop . Booz Allen Hamilton Inc. 134 National Business Parkway Annapolis Junction, MD 20701 Tel (301) 543-4665 [email_address] Paul Brown Associate
  • 2.
  • 3. Biological Information Paul Brown 9/21/09 Need to verify all these.
  • 4. Biology + Computer Science = Bioinformatics http://bioinformatics.ubc.ca/about/what_is_bioinformatics A Y N A R N A N R N Y A Y N N R N A A N R N
  • 5.
  • 6.
  • 7.
  • 8.
  • 9.
  • 10.
  • 11. Smith-Waterman Algorithm - A Y N A N A N A - 0 0 0 0 0 0 0 0 0 A 0 2 1 0 2 1 2 1 2 N 0 1 1 3 2 4 3 4 3 A 0 2 1 2 5 4 6 5 6 N 0 1 1 3 4 7 6 8 7 A 0 2 1 2 5 6 9 8 10 N 0 1 1 3 4 7 8 11 10 R 0 0 0 2 3 6 7 10 10 A 0 2 1 1 4 5 8 9 12
  • 12.
  • 13.