LECTURE 11-Genomics and Bioinformatics Time machines and function

LECTURE 11-Genomics and Bioinformatics Time machines and function

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Unformatted text preview: Genomics and bioinformatics summary 1. Gene finding: computer searches, cDNAs, ESTs, 1. Microarrays 2. Use BLAST to find homologous sequences 3. Multiple sequence alignments (MSAs) 4. Trees quantify sequence and evolutionary relationships 5. Protein sequences are evolutionary clocks 6. Some public databases and protein sequence analysis tools Finding genes -- computer searches Computer searches locate most genes in prokaryotes, Archeae, and yeast, but only ~ 1/3 of human genes are identified correctly. Criteria Protein start, stop signals, splicing signals . . . Codon bias Comparisons to other genomes (mouse, rat, fish, fly, mosquito, worm, yeast . . .) Some hard problems: small genes, post-translational modifications, unique genes, spliced genes, alternative splicing, gene rearrangements (e.g. IgGs) . . . Finding genes -- cDNA synthesis Synthesizing cDNA (complementary DNA) 1. Extract RNA 1. Hybridize polyT primer 1. Synthesize DNA strand 1 using reverse transcriptase. 4. Fragment RNA strand using RNaseH. 5. Synthesize DNA strand 2 using DNA pol Sequences of random cDNAs provide ESTs (Expressed Sequence Tags) Microarrays quantify expressed genes by hybridization 1. Label cDNAs with red fluorophore in one condition and green fluorophore in another reference condition. 2. Mix red and green DNA and hybridize to a microarray. Red genes enriched in reference Yellow genes (green + red) = Green genes enriched in experiment Each spot is a different synthetic oligonucleotide complementary to a specific gene. Cluster analysis identifies patterns of gene...
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LECTURE 11-Genomics and Bioinformatics Time machines and function

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