biocomputation : comparative genomics
DESCRIPTION
Biocomputation : Comparative Genomics. Tanya Talkar Lolly Kruse Colleen O’Rourke. DNA . Junk DNA. Conserved DNA. What is Biocomputation ?. Four Main Parts. Biomolecular computation Biological Computation Computational Biology Bioinformatics. Bioinformatics:. Sequence Analysis. - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/1.jpg)
Biocomputation: Comparative Genomics
Tanya TalkarLolly KruseColleen O’Rourke
![Page 2: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/2.jpg)
DNA
![Page 3: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/3.jpg)
![Page 4: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/4.jpg)
JunkDNA
ConservedDNA
![Page 5: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/5.jpg)
What is Biocomputation?
Statistics
Computer Science
Molecular Biology
![Page 6: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/6.jpg)
Four Main Parts Biomolecular computation Biological Computation Computational Biology Bioinformatics
![Page 7: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/7.jpg)
Bioinformatics:
Biology
Computer Science
Information
Technology
![Page 8: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/8.jpg)
Sequence Analysis Very Functional! Compare DNA between Species Small Fragments Return full sequence
![Page 9: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/9.jpg)
Computational Genomics Needleman – Wunsch
Not used much More Mapped Genomes =
Computational Genomics!
![Page 10: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/10.jpg)
Alignment
![Page 11: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/11.jpg)
Global Alignment:Needleman - Wunsch O(N3) Fewest edit operations Similar strings
![Page 12: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/12.jpg)
Local AlignmentSmith - Waterman O(N2) Dissimilar strings Find high similarity regions
![Page 13: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/13.jpg)
Comparison
![Page 14: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/14.jpg)
S1 P Q R A X A B C S T V Q
S2 X Y A X B A C S L T
A X A B C S
A X B A C S
![Page 15: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/15.jpg)
S1 A X A B _ C S
S2 A X _ B A C S
Score 2 2 -1 2 -1 2 2
![Page 16: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/16.jpg)
Advantages:Global Alignment
![Page 17: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/17.jpg)
Advantages:Local Alignment
![Page 18: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/18.jpg)
BLAST• Basic Local Alignment Search Tool• FASTA
![Page 19: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/19.jpg)
Improvements Increased Speed Locate initial alignment hot spots Statistical significance
![Page 20: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/20.jpg)
Terminology Segment Pairs Locally maximal segment pairs Maximal segment pairs
![Page 21: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/21.jpg)
How it works Query sentence, P Database
Must have score over C! Multiple segment pairs combined
A B C D E F G
A G C B F D EB E D G A F BG F B E D C A
![Page 22: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/22.jpg)
How it works Extends each hit Done efficiently Truncates Doesn’t find all pairs
![Page 23: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/23.jpg)
Proteins Fixed length, W Words above threshold Each hit extended
![Page 24: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/24.jpg)
DNA Word List Exact matches NOT dynamic programming
![Page 25: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/25.jpg)
Scoring Blosum62 Matrix Match (+2), Mismatch (-3),
Gaps penalized
![Page 26: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/26.jpg)
Substitution Matrix Represents Scoring Functions
![Page 27: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/27.jpg)
Multiple Sequence Alignment
![Page 28: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/28.jpg)
Methods of MSA Progressive Alignment Construction Iterative Methods Hidden Markov Models Genetic Algorithms and Simulated
Annealing
![Page 29: Biocomputation : Comparative Genomics](https://reader035.vdocuments.site/reader035/viewer/2022062521/568163a3550346895dd4a6ba/html5/thumbnails/29.jpg)
Comparative Genomics Compare Species
Find Evolutionary Significances! Low Level High Level
Importance of Non Coding DNA