PASA Pipeline - Rice Genome Annotation Project

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FL-cDNAs and ESTs “Gold standard” for gene structure resolution • Introns and exons via spliced alignment Direct evidence for: • Alternative splicing • Untranslated regions (UTRs) • Polyadenylation sites
The PASA Pipeline Automate incorporation of transcript alignments into gene structure annotations It was originally developed to refine gene structures in Arabidopsis as part of our Arabidopsis re-annotation effort. Since that time, we’ve expanded the pipeline and applied it to a range of other organisms at TIGR, now with a special focus on Rice.
Page 1 and 2: -2 Transcript Alignment Assembly an
Page 3: Topics Outline Overview of the PAS
Page 7 and 8: Additionally Found Uses of PASA Au
Page 9 and 10: Transcript Sequences Seqclean Align
Page 11 and 12: Transcript Sequences PASA Pipeline
Page 13 and 14: Transcript Sequences PASA Pipeline
Page 15 and 16: Alignment Assembly Maximize evidenc
Page 17 and 18: Alignment Assembly using PASA: Prog
Page 19 and 20: PASA Algorithm Containments preclu
Page 21 and 22: PASA Algorithm Find Maximal Assembl
Page 23 and 24: Incorporation of PASA assemblies in
Page 25 and 26: FL-assembly-based updates Existing
Page 27 and 28: Alternative Splicing (incompatible
Page 29 and 30: Enhancements: Gene Merging (FL-cDNA
Page 31 and 32: Enhancements: Gene Existing gene Sp
Page 33 and 34: Want more aggressive updates? Besi
Page 35 and 36: Example Application of PASA to Rice
Page 37 and 38: Gene Comparison Summary (Counting G
Page 39 and 40: Examining Updates (clicking any lin
Page 41 and 42: Examples of Classified Updates FL a
Page 43 and 44: EST extends UTRs EST extends protei
Page 45 and 46: A tool for Studying Alternative Spl
Page 47 and 48: PASA Documentation http://pasa.sf.n
Page 49: QUESTIONS?

PASA Pipeline - Rice Genome Annotation Project

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