BIOINFORMATICS and Data analysis ppt 202

Bioinformatics

1. 1 Bioinformatics

2. Biological Databases

3. What we expect from a database..!! Sequence, functional, structural information, related bibliography Well Structured and Indexed Well cross-referenced (with other databases) Periodically updated Tools for analysis and visualization

4. Biological Databases Sequence databases Structure databases

5. Sequence databases Nucleotide databases Protein databases

6. Sequence databases

7. Nucleotide databases International Nucleotide Sequence Database Collaboration (INSDC) NCBI EMBL DDBJ

8. Standard contents of a sequence database Sequences Accession number References Taxonomic data Annotation/curation Keywords Cross-references Documentation

9. Practical section

10. Gene view

11. Gene sequence

12. Page configure

13. Mutation view

14. Choose a variant

15. Open the reference sequence

16. Population genetics

17. Flanking sequence

18. Choose the sequence for primer design

19. By using primer 3 (online)

20. Page view

21. Paste your sequence

22. You can took the sequence to a word file to count the total size of your sequence : TGTGTTGTTCCCCTATTGGCTAGGGTTGGACCACACCGTCTGAGCTAATTGTTACTGGCT ATTTTAAAGAGAGCAGGGGTAAGAGCCGGATTGGCAGGGTAAGTAGTTTGGCAGGAAGGA CGGTCACAGAACAGGTGACTCAGGATGACTCAGGTCAGAG Y AGGTGACCAGTGGTGACTC AGTTCGGAGCAGGTGATAGAAGCTAGGAGGGGGTTGTTTACTGAAACTAGGGGCAAGGAG ACGAAGAGAACATGAAAGTTAAACTTTAAGATGAAGAACAAAGCTGAACATACTGATGCA = 300bp

23. output

24. We chose the primer number 4 which is give the largest product size is =239 bp SNP location :161

25. step3 BLAST

26. Basic local alignment search tool view

27. Results

28. STEP4 : Choose the restriction enzyme By using web cutter

29. Put the short sequence at the box and analyze it ,,, (CGGTCACAGAACAGGTGACTCAGGATGACTCAGGTCAGAG Y AGGTGACCAGTGGTGACTC) This the sequence we will enter it it’s 60 bp and our SNP found at 41 bp so we chose the enzyme that cut near it :

30. Inter the sequence

31. results view

32. We chose the enzyme ( Mn1I) that cut at 41 ( c/ ctc ) mutant type Or( hae III ) that at 40 ( gg /cc) wild type So know we can apply this in lab work. Also there anther online application that can display the restriction enzyme like a map …

33. NEB cutter

34. H.W Design a suitable primer for rs180113 variant and give a possible restriction enzyme to be used for RFLP-PCR genotyping method.

35. THE END