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Bioinformatics/HPC. Students Adda Zachary Deema Al Ghanim Horsley Jacqueline Sandrick Daniel. Mentors Xiaoming G ao Xinjun Zhang Thilina Gunarathne Supervised by Dr.Judy Qiu. Sequence Alignment. A way of arranging the biological sequences to identify regions of similarity

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bioinformatics hpc

Bioinformatics/HPC

Students

Adda Zachary

DeemaAl GhanimHorsley JacquelineSandrickDaniel

  • Mentors
  • XiaomingGao
  • XinjunZhang
  • ThilinaGunarathne
  • Supervised byDr.JudyQiu
sequence alignment
Sequence Alignment
  • A way of arranging the biological sequences to identify regions of similarity
  • Pairwise alignment
    • Find the best matching alignments of two query sequences
  • Multiple Sequence Alignment
    • Alignment of 3 or more biological sequences
    • Computationally difficult
slide3

MDS

Pairwise

Sequence Alignment

Sequences

Dissimilarity Matrix

Visualization

Pairwise Clustering

http://salsaweb.ads.iu.edu/salsa/

phylogenetics
Phylogenetics
  • Study ofevolutionaryrelatedness among various groups of organisms
  • Phylogenetic tree
    • Tree of life
  • Finding the correlations between Phylogenetic trees and the clustering approach
additional software
Additional Software
  • PHYLIP (PHYLogenyInference Package)
    • Software available in IU Quarry
    • Inputs
      • Distance Matrix
      • Gene sequences
  • Clutalw
    • Available in IU BigRed
    • Multiple sequence alignment
    • Can generate data files for PHYLIP