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4: Comparative Genomics I- Genome Annotation

Last updated

Mar 17, 2021
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- 3.7: Probabilistic Foundations of Sequence Alignment
- 4.1: Introduction

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In this chapter we will explore the emerging field of comparative genomics, primarily through examples of multiple species genome alignments (work done by the Kellis lab.) One approach to the analysis of genomes is to infer important gene functions through applying an understanding of evolution to search for expected evolutionary patterns. Another approach is to discover evolutionary trends by studying genomes themselves. Taken together, evolutionary insight and large genomic datasets offer great potential for discovery of novel biological phenomena.

4.1: Introduction
4.2: Conservation of genomic sequences
4.3: Excess Constraint
4.4: Diversity of evolutionary signatures- An Overview of Selection Patterns
4.5: Protein-Coding Signatures
4.6: microRNA (miRNA) Gene Signatures
How do we find evolutionary signatures for miRNA genes and their targets, and can we use these to gain new insights on their biological functions? We will see that this is a challenging task, as miRNAs leave a highly conserved but very subtle evolutionary signal.
4.7: Regulatory Motifs
Another class of functional element that is highly conserved across many genomes contains regulatory motifs. A regulatory motif is a highly conserved sequence of nucleotides that occurs many times throughout the genome and serves some regulatory function. For instance, these motifs might characterize enhancers, promoters, or other genomic elements.
4.8: Further Reading
4.9: Tools and Techniques
Bibliography

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