lecture_notes:05-27-2015
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Table of Contents
Genome Annotation
Repeat Annotation
Masking
- Done to facilitate conventional gene annotation efforts.
- Helps avoid false SNP calls and mapping ambiguities.
- Hard Masking: replacing repeats with Ns {ACGTNNNNNNNNNATGG}
- Soft Masking: replacing repeats with lowercase {ACGTtagtagtagATGG}
Repeat Annotation
- Different types of repeats can be studied along with their levels of activity (evolutionary analyses)
Types of Repeats
- low-complexity sequence: microsatellites, homopolymers, etc.
Transposable Elements
- class 1: retrotransposon; “copy & paste”; LTR, LINES, SINES
- class 2: DNA transposons; “cut & paste”; subclass 1 and subclass 2
Repeat Content
- Does not necessarily correlate with genome size
- some correlation within the same group
Tools
- Homology: RepeatMasker
- denovo: RepeatModeler, WindowMasker, RepeatScout, Piler
- denovo from reads: REPdenovo, TEDNA
- NOTE: denovo tools run risk of false positives from highly conserved protein-coding genes.
Gene Annotation
Evidence-driven Annotation
- protein information, EST, RNA-Seq
Ab initio Gene Prediction
- doesn't require evidence data
- requires training for organism of interest
- most find single most likely CDS
- do not report UTR's (incomplete gene model)
- does not accommodate spliceoforms
- requires high-quality assembly (scaffold N50 ≈ avg gene size)
Combined Approach
- challenge of collating different models and sources of evidence.
Annotation Metrics
- Sensitivity, specificity, accuracy, AED
- AED = 1 - ACC = 1 - .5(Sensitivity+specificity)
- AED useful for identifying low quality inconsistent annotations (can be manually curated later)
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lecture_notes/05-27-2015.1432815836.txt.gz · Last modified: 2015/05/28 05:23 by emfeal
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