1. Group Medicago Basic Project: Gene expression in yeast Advanced Bioinformatics

2. Members Jente Ottenburghs Lifei Li Yuebang Yin Nick Brouwers

3. Members: Yuebang During the day: Working on farm During the evenings: programming

4. Members: Jente, Lifei & Nick During the day: Programming During the evenings: Preparing for another day of programming

5. Progress: Pipeline Fastq-file Bam-file genome.fa Transcripts.gtfgenome.fa Fasta-file Amazing Output Tophat Cufflinks Gtf_to_fasta Perl Scripts

6. Progress so far... Making the Big Hash Table (Nick, Yuebang & Lifei) Codon usage bias (Jente) Graphical Output R (Jente)

7. The Big Hash Table Data extraction of GTF-file and Fasta-file: Hash table with array Gene ID: Value1 Value2... KeyValue = Array

8. The Big Hash Table From the FASTA we use/determine: Gene_id Sequence length GC content Codon usage From the GTF we use/determine: Gene_id Expression level Inter-transcript size

9. The Big Hash Table GTF Hash TableFasta Hash Table One Big Hash Table User determines Output The Next Step

10. Codon Usage Scripts for calculation of: Relative Synonymous Codon Usage (RSCU) Effective number of codons (NC)

11. Codon Usage

12. Future Challenges Store more data in the table Let the user determine the output (Perl) Produce graphical output (R)

13. The end! (but now half way)