The hitchhiker's guide to bioinformatics

1. Amit Kumar Yadav, PhD
Drug Discovery Research Center (DDRC)
Translational Health Science and Technology
Institute (THSTI)
3rd Nov
2015

2. DISCLAIMER
•This is not a class. Notes aren't helpful,
discussions are !!!
•Most are conceptual analogies, not accurate
details !!!
•Focus is on understanding, not subject
coverage !!!

3. WHAT IS BIO-INFORMATICS ?
WHAT IS COMPUTATIONAL BIOLOGY?
Biology
Chemistry
Mathematics
Computer
Science
Statistics

4. WHAT DOES A BIO-INFORMATICIAN DO ?

5. DNA
protei
n
mRNA
tRNA

6. NEW AGE BIOLOGY = SYSTEMS BIOLOGY !

8. CREATING THE MAP = SEQUENCING
THINGS !

9. FASTA FILE

10. SEQUENCE ALIGNMENT

11. SEQUENCE ALIGNMENT

12. DATABASE RESOURCES

14. BLAST SEARCH

15. DOMAIN AND STRUCTURE DATABASES

16. ASSEMBLING 3 BILLION PIECES !!!

17. DNA SEQUENCING

18. TRANSCRIPTOMICS (RNA-SEQ)

19. TRANSCRIPTOMICS (RNA-SEQ)

21. ONE GENOME…MANY PROTEOMES
Perhaps not…
they still have a
dynamic
“proteome” code
to break. They
cannot hit a
moving target

22. MILESTONES

23. SHOTGUN PROTEOMICS

24. SHOTGUN PROTEOMICS ALGORITHM
Intensity of
matching
peaks
Continuity of
y-ions & b-
ions
Neutral
losses &
Immonium
ions
Fragment
mass error
sensitive
scoring

25. PROTEIN IDENTIFICATION?
Protein Assembler

27. SIMILAR PROTEOMES … DIFFERENT
PHENOTYPES ?
OK…I will
wait to see
if they can
break the
PTM code

30. biological processes are modular
!!!

31. How not to collaborate !
I’m the brain,
he’s the brawn
Bioinformatics
/
Computational
Lab
Cell/Molecular
Biology Lab

32. THANK YOU !

33. TAKE HOME MESSAGE
• Bioinformatics is NOT biology or informatics, its
both
• Genomics, transcriptomics, proteomics = large
scale studies of biomolecules DNA, RNA and
proteins
• Systems biology = holistic views of biological
phenomenon = mountains of data
• Algorithm development, Automated analysis,
Database development and Data management =
data science

34. ACKNOWLEDGEMENTS
• Dr. Rekha Kumari
• Dr. Richa Misra
• ICGEB, DDRC, THSTI
• DBT-IYBA