**This is an old revision of the document!** ----
====== 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)
