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Similar to Lecture1 1 Perl for bioinformatics Davide Pisani & James Cotton
Lecture1 1 Perl for bioinformatics Davide Pisani & James Cotton
- 1. Bioinformatics Programming (PerlProgramming) 2010 Davide Pisani
- 2. Bioinformatics • Usingcomputers to store, organise and interpret biological data • In particular, data from high-throughput technologies (-omics)
- 3. High-throughput technologies •DNA & Protein sequences and structure (genomics & Proteomics) • Yeast two-hybrid screens (interactomics) • Microarrays (transcriptomics) • Metabolic networks (metabolomics)
- 4. How much sequencedata is there? 1371published complete genomes 188 ongoing archaeal genomes 4941 Bacterial ongoing genomes 1599 Ongoing eukaryotic genomes 242 metagenomes
- 5. How much datain each genome? ftp://ftp.ncbi.nih.gov/refseq/release/
- 6. The human genome ftp://ftp.ncbi.nih.gov/refseq/release/
- 7. The human genome ftp://ftp.ncbi.nih.gov/refseq/release/
- 8. The human genome ftp://ftp.ncbi.nih.gov/refseq/release/ etc.. (70 base pairs per line, 57 lines per page = 3990 bases/page Chromosome 1 is (about) 247,249,719 bases long i.e. 62,000 pages Whole genome (3.2 x 109) = 802,000 pages
- 9. Genome Base pairsNo. of Genes Phi-X 174 5,386 10 Nanoarchaeum equitans 490,885 552 E. coli 4,639,221 4,377 Saccharomyces 12,495,682 5,800 cerevisiae Drosophila melanogaster 122,653,977 13,379 Homo sapiens 3.2 x 109 30,000 Protopterus aethiopicus 1.3 x 109 ? Psilotum nudum 2.5 x 1011 ?20-25,000 Amoeba dubia 6.7 x 1011 ?
- 10. Genbank contains muchmore than just sequence data Information on the Organism, the gene, where it is expressed and so forth.
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