Group Medicago Basic Project: Gene expression in yeast Advanced Bioinformatics

Members Jente Ottenburghs Lifei Li Yuebang Yin Nick Brouwers

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

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

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

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

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

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

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

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

Codon Usage

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

The end! (but now half way)