1. Bioinformatics What is a genome? How are databases used? What is a phylogentic tree?

2. The Genome Every organism, including man, is specified by a genome. A genome is composed of DNA segments, called genes. Genes code for proteins http://www.bio.tamu.edu/synecho/progress.html

3. Bioinformatics is used for… Determining evolutionary relationships between organisms Looking at locations of particular genes Crop/Pharmaceutical Bioengineering Medical research

4. Bioinformatics is used for…. Making new drugs Crop bioengineering Gene sequencing Making phylogenetic trees

5. The Human Genome Project Began in the year 2000, published report in 2001 (Nature) Goal: to sequence all 20,000-25,000 genes on all the chromosomes in the human body New research is focusing on bioenergy— –developing plant feedstocks (fast-growing plants bred to produce electricity or liquid fuels) –using microorganisms (like bacteria) to break down cellulose in plant cell walls –converting sugars into biofuels.

6. Databases are… a storehouse of organized, indexed computerized data

7. Databases are used to … locate a gene within a sequence predict protein structure and/or function cluster protein sequences into families of related sequences view and analyze the data on millions of genomes

8. Step 1: Go to IMG Home Page Go to Find Genes

9. Step 2: Click on BLAST

10. Step 3: Copy and paste a nucleotide or protein sequence This is your query sequence

11. Step 4: BLAST sequence Take the top hit and click on it: this will give you a list of the genomes with the most similarity to your query sequence

12. Step 5: Click on the top hit

13. Step 6: Look at Gene Detail OID number Name of protein

14. Look at “gene neighborhood” Red shows query gene

15. Step 7:Click on IMG Genome BLAST

16. Step 8: Choose a Phylum or organism to BLAST against

17. Step 9: Set Maximum E-value Run BLAST The lower this number is, the more significant the alignment is between the query sequence and the other genomes you are comparing it against A low E Value shows genes with the most homology Run BLAST

18. Look at Genome Blast Results

19. Blast hits on a particular sequence

20. Look at: Alignment and E-values O= orthologs- genes from different species which are similar P= paralogs- genes from the same species which are similar

21. For a detailed view of alignment,click on Do Alignment: Letters denote amino acids; colors denote type of amino acid Dashed lines indicate deletions Look down this column- what do you notice?

22. Categories of amino acids

23. Homologs Gene sequences that are similar and show a close evolutionary relationship Two types of homologs: –Paralogs- similar gene sequences between members of the same species –Orthologs- similar gene sequences between 2 different species

24. 10. Click on the hits with the best alignment

25. 11. Add Selections to Gene Cart

26. 12. Click: Show Gene Neighborhoods

27. 13. Gene of interest is shown in red Look at colored genes next to gene of interest Gene of interest

28. 14. To make a phylogenetic tree, go to Phylogeny.fr Copy and Paste amino acid sequence Click submit

29. 15. Click Blast Explorer Paste sequence Click submit

30. A phylogenetic tree of cyanobacteria with homology for a particular gene sequence