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Advanced Bioinformatics

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

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Advanced Bioinformatics

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

  2. Members • JenteOttenburghs • 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 evenings: Preparing for another day of programming During the day: Programming

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

  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)

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