1. Bioinformatics

2. Identify what is Bioinformatics. Explain sequence databases
By the end of this topic, the student will be able to
Identify what is Bioinformatics.
Explain sequence databases
Identify and align nucleotide sequences using BLAST
Translate and align Protein sequences using BLAST
Interpret the data of Bioinformatics.

3. What is Bioinformatics?

4. What is Bioinformatics?
The use of computers to collect, analyze, and interpret biological information at the molecular level.
Analyze
Understand
Organize
Info.
Large Macromolecules Biological Databases

5. What skills are needed? Well-grounded in one of the following areas:
Computer science
Molecular biology
Statistics

6. Bioinformatics works at:
DNA level:
DNA sequence alignment; gene prediction; gene evolution;…
RNA level:
Study of gene expression; transcription mechanism; post-transcription modification;…

7. Protein level: protein 2D and 3D structure prediction;
protein active site prediction;
protein-protein interactions;
protein-DNA interactions;…

8. The computer and molecular databases are a necessary, integral part of this entire process.

9. What are sequence databases?
Databases are an organized way to store and organize the tremendous amount of sequence information accumulating worldwide.
Most databases have their own specific format.

10. Progress of the Human Genome Project
From June April 2003

11. What are sequence databases?
North America: the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM), at the National Institute of Health (NIH).

12. Europe: the European Molecular Biology Laboratory (EMBL), the European Bioinformatics Institute (EBI), and the Swiss Institute of Bioinformatics’ (SIB). There are also the expert Protein Analysis System (ExPasy),the SWISS-PROT amino acid sequence databases.

13. Asia: The National Institute of Genetics (NIG) & DNA Data Bank of Japan (DDBJ).

14. + Results Biologist Databases PDB: Protein data bank GenBank PDB
PubMed
Results
Databases
PDB: Protein data bank

15. National Center for Biotechnology
Information (NCBI)

16. Steps Of work
Step one

17. Go Identify a gene sequence by BLAST

18. BLAST is…
Basic Local Alignment Search Tool
NCBI's sequence similarity search tool
80,000 searches per day

20. Feed your sequence to the space provided then choose blastN
AUGGUGCAUCUGACUCCUGAGGAGAAGUCUGCCGUUACUGCCCUGUGGGGCAAGGUGAACGUGGAUGAAGUUGGUGGUGAGGCCCUGGGCAGGCUGCUGGUGGUCUACCCUUGGACCCAGAGGUUCUUUGAGUCCUUUGGGGAUCUGUCCACUCCUGAUGCUGUUAUGGGCAACCCUAAGGUGAAGGCUCAUGGCAAGAAAGUGCUCGGUGCCUUUAGUGAUGGCCUGGCUCACCUGGACAACCUCAAGGGCACCUUUGCCACACUGAGUGAGCUGCACUGUGACAAGCUGCACGUGGAUCCUGAGAACUUCAGGCUCCUGGGCAACGUGCUGGUCUGUGUGCUGGCCCAUCACUUUGGCAAAGAAUUCACCCCACCAGUGCAGGCUGCCUAUCAGAAAGUGGUGGCUGGUGUGGCUAAUGCCCUGGCCCACAAGUAUCACUAA

22. AUGGUGCAUCUGACUCCUGAGGAGAAGUCUGCCGUUACUGCCCUGUGGGGCAAGGUGAACGUGGAUGAAGUUGG

25. Repeat same steps with this sequence
AUGGUGCAUCUGACUCCUGUGGAGAAGUCUGCCGUUACUGCCCUGUGGGGCAAGGUGAACGUGGAUGAAGUUGGUGGUGAGGCCCUGGGCAGGCUGCUGGUGGUCUACCCUUGGACCCAGAGGUUCUUUGAGUCCUUUGGGGAUCUGUCCACUCCUGAUGCUGUUAUGGGCAACCCUAAGGUGAAGGCUCAUGGCAAGAAAGUGCUCGGUGCCUUUAGUGAUGGCCUGGCUCACCUGGACAACCUCAAGGGCACCUUUGCCACACUGAGUGAGCUGCACUGUGACAAGCUGCACGUGGAUCCUGAGAACUUCAGGCUCCUGGGCAACGUGCUGGUCUGUGUGCUGGCCCAUCACUUUGGCAAAGAAUUCACCCCACCAGUGCAGGCUGCCUAUCAGAAAGUGGUGGCUGGUGUGGCUAAUGCCCUGGCCCACAAGUAUCACUAA

27. So we can Conclude that the sequences are aligned with the normal sequences in the database
Try your self

28. Let’s try to align 2 sequences :
One from a healthy person & another from
a sickle cell anemia patient .

29. Step Two

30. Choose blast N Report your finding.
Go Align Nucleotide sequences to compare:
Choose blast N
Report your finding.

32. Try your self

33. Step Three

34. Try your self Go translate both sequences in previous slides
Try your self

35. Step Four

36. Go Allign Protein sequences (Open reading frames) to compare:
Choose blast p
Met V H L T P E E K S A V T A L W G K V N V D E V G G E A L G R L L V V Y P W T Q R F F E S F G D L S T P D A V Met G N P K V K A H G K K V L G A F S D G L A H L D N L K G T F A T L S E L H C D K L H V D P E N F R L L G N V L V W C W P I T L A K N S P H Q C S C L S E S G G W C G Stop C P G P Q V S L
Met V H L T P V E K S A V T A L W G K V N V D E V G G E A L G R L L V V Y P W T Q R F F E S F G D L S T P D A V Met G N P K V K A H G K K V L G A F S D G L A H L D N L K G T F A T L S E L H C D K L H V D P E N F R L L G N V L V W C W P I T L A K N S P H Q C S C L S E S G G W C G Stop C P G P Q V S L
Report your finding.

38. Normal Hemoglobin beta protein sequence
MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVASALAHKYH
Hemoglobin S beta chain
MVHLTPVEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVASALAHKYH

39. Try your self

40. Extended Modular Program