Advanced Bioinformatics

Advanced Bioinformatics Group Medicago Basic Project: Gene expression in yeast

Members • JenteOttenburghs • Lifei Li • Yuebang Yin • Nick Brouwers

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

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

Progress: Pipeline Fastq-file genome.fa Tophat Bam-file Cufflinks Transcripts.gtf genome.fa Gtf_to_fasta Amazing Output Fasta-file 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 ... Key Value = 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 Fasta Hash Table GTF Hash Table One Big Hash Table The Next Step User determines Output

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)

Advanced Bioinformatics