Learning Objectives
282 words
1 min read
Visual companion
Python
Type and operator map
Python Week 1: the first filter for runtime behavior
View
Revision summary
What this note is really saying
Short form
# Learning Objectives - Analyze genomic data for functional elements - Understand variant calling pipeline - Apply comparative genomics ## 1. Genome Annotation Identifying functional elements: gene prediction (ab initio with HMM or evidence-based), repeat annotation, ncRNA identification, regulatory region annotation.
Learning Objectives
- Analyze genomic data for functional elements
- Understand variant calling pipeline
- Apply comparative genomics
1. Genome Annotation
Identifying functional elements: gene prediction (ab initio with HMM or evidence-based), repeat annotation, ncRNA identification, regulatory region annotation.
2. Variant Calling
Types: SNPs (single base change), indels (small insertions/deletions), CNVs (large duplications/deletions), SVs (inversions, translocations).
Pipeline: Align reads (BWA, Bowtie) -> Sort/Mark duplicates (SAMtools) -> Call variants (GATK, FreeBayes) -> Filter -> Annotate (SnpEff, VEP).
3. Comparative Genomics
Comparing genomes across species reveals conserved regions (functionally important), lineage-specific changes, evolutionary rates (dN/dS ratio).
Q1: How are genes predicted in a genome?Ab initio: train HMM on known genes, predict new ones based on sequence patterns (start/stop codons, splice sites, codon usage). Evidence-based: align RNA-seq transcripts. Combined is most accurate. Q2: What is a SNP and how is it called?Single Nucleotide Polymorphism: position where individuals differ by one base. Called by aligning reads to reference and finding positions where many reads disagree at high quality. Q3: What is the dN/dS ratio?dN = non-synonymous substitutions (change amino acid), dS = synonymous (silent). dN/dS > 1 = positive selection, < 1 = purifying selection (conservation), = 1 = neutral. Q4: What is the GATK best practices pipeline?Preprocess reads (align, dedup, BQSR) -> Call variants (HaplotypeCaller) -> Filter (VQSR) -> Annotate and analyze. Industry standard for variant calling. Q5: Homozygous vs heterozygous variants?Homozygous: both chromosomes have variant (all reads show variant). Heterozygous: one variant, one reference (~50% reads show variant). Detected by allele balance statistics. Join Discord PreviousGenome AssemblyNextProtein Structure & Prediction