11.genes - Genomics and bioinformatics summary

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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
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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) . . .
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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)
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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.
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11.genes - Genomics and bioinformatics summary

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