PASA Pipeline - Rice Genome Annotation Project

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Full-length cDNAs Provide Complete Gene Structures (hence, full-length Assemblies too!) Genomic DNA Gapped Alignment Poly-A site Full-length cDNA AAAAAAAAAAAAAA •cDNA-genome spliced alignment •ORF reconstruction based on the joined exons. •UTRs identified. •Automated process
FL-assembly-based updates Existing model: UTR Different Introns/Exons UTR FL-assembly-based model: ::FL-assembly-based model replaces the existing model = CDS = cDNA
Page 1 and 2: -2 Transcript Alignment Assembly an
Page 3 and 4: Topics Outline Overview of the PAS
Page 5 and 6: The PASA Pipeline Automate incorpo
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: Incorporation of PASA assemblies in
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?

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