1 / 29

CS 451 / 558

CS 451 / 558. Week 3, Tue. In class exercises – Perl 3. Write a program to reverse transcribe RNA to DNA (4.5 from the book). In class exercises – Perl 4. Read two files of data (sequence1.fa and sequence2.fa). Print the contents of the first, then the contents of the 2 nd .

dirk
Download Presentation

CS 451 / 558

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. CS 451 / 558 Week 3, Tue

  2. In class exercises – Perl 3 • Write a program to reverse transcribe RNA to DNA (4.5 from the book)

  3. In class exercises – Perl 4 • Read two files of data (sequence1.fa and sequence2.fa). Print the contents of the first, then the contents of the 2nd. (4.6 from the book)

  4. In class exercises – Perl 5 • Write a program to read a file, then print its lines in reverse order (last line first). • Options • reverse • push/pop/shift/unshift (possibly with loops) (4.7 from the book)

  5. Homework / Projects • Homework due next Thurs • Projects • See website (discuss in class / see dates) • Grad / undergrad projects are distinct

  6. Homology

  7. Homology • a similarity often attributable to common origin • likeness in structure between parts of different organisms due to evolutionary differentiation from a corresponding part in a common ancestor

  8. Homology • a similarity often attributable to common origin • likeness in structure between parts of different organisms due to evolutionary differentiation from a corresponding part in a common ancestor • Bat’s wing and human’s arm are homologous • NOT bee’s wing

  9. Homology • a similarity often attributable to common origin • likeness in structure between parts of different organisms due to evolutionary differentiation from a corresponding part in a common ancestor • Bat’s wing and human’s arm are homologous • NOT bee’s wing

  10. Homology • a similarity often attributable to common origin • likeness in structure between parts of different organisms due to evolutionary differentiation from a corresponding part in a common ancestor • Bat’s wing and human’s arm are homologous • NOT bee’s wing

  11. Sequence Homology acgt

  12. Sequence Homology acat g  a acgt

  13. Sequence Homology acat g  a acgt c agt

  14. Sequence Homology acacct + cc acat g  a acgt c agt

  15. Sequence Homology acacct + cc acat g  a acat acgt agt c agt a  g ggt

  16. Sequence Homology acacct + cc acat g  a acat acacct aca--t a-g--t g-g--t acgt agt c agt a  g ggt

  17. Sequence Homology acacct + cc acat g  a acat acacct aca--t a-g--t g-g--t acgt agt c agt a  g ggt

  18. Comparing sequences AATCTATA AAGATC AATCTATA AAGATC AATCTATA AAGATC

  19. Comparing sequences AATCTATA AAGATC AATCTATA AAGATC AATCTATA AAGATC AATCTATA AAG-AT-C AATCTATA AA-G-ATC AATCTATA AA--GATC

  20. Comparing sequences AATCTATA AAGATC AATCTATA AAGATC AATCTATA AAGATC AATCTATA AAG-AT-C AATCTATA AA-G-ATC AATCTATA AA--GATC --AATCTATA AAGATC----

  21. Comparing sequences AATCTATA AAGATC AATCTATA AAGATC AATCTATA AAGATC AATCTATA AAG-AT-C AATCTATA AA-G-ATC AATCTATA AA--GATC --AATCTATA AAGATC---- AATCTATA---- -----A-AGATA

  22. Comparing sequences AATCTATA AAGATC AATCTATA AAGATC AATCTATA AAGATC AATCTATA AAG-AT-C AATCTATA AA-G-ATC AATCTATA AA--GATC --AATCTATA AAGATC---- AATCTATA---- -----A-AGATA terminal gaps internal gaps

  23. Metrics on Strings • Hamming distance • number of positions at which the corresponding symbols are different • Edit distance (Levenshtein distance) • minimum number of single-character edits (i.e. insertions, deletions or substitutions) required to change one word into the other .

  24. Metrics on Strings • Hamming distance • number of positions at which the corresponding symbols are different • Edit distance (Levenshtein distance) • minimum number of single-character edits (i.e. insertions, deletions or substitutions) required to change one word into the other • Contrast this with similarity scores, such as +1/0 or +1/-1.

  25. How to find best alignment(the one with the best similarity score) • Dot Plot

  26. How to find best alignment(the one with the best similarity score) • Dot Plot ACGTAAA Where are the A’s? (pseudocode / perl)

  27. How to find best alignment(the one with the best similarity score) • Dot Plot ACGTAAA CGTACGT Print 2D array of single-letter matches

  28. How to find best alignment(the one with the best similarity score) • Dot Plot ACGTAAA Where are the AA’s? (pseudocode / perl)

  29. How to find best alignment(the one with the best similarity score) • Dot Plot ACGTAAA CGTACGT Print 2D array of two-letter matches (Homework 1)

More Related