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Maize genome annotation project Agry 60000 group 2. Karthik Padmanabhan Shuai Chen Shaylyn Wiarda. 12/06/12. workflow. MegaBLAST Gene Prediction on unmasked sequence AUGUSTUS FGENESH GeneMark CpG island prediction Repeat Masker Gene Prediction on masked sequence AUGUSTUS FGENESH - PowerPoint PPT Presentation
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MAIZE GENOME ANNOTATION PROJECTAGRY 60000GROUP 2
KARTHIK PADMANABHANSHUAI CHENSHAYLYN WIARDA
12/06/12
WORKFLOW1. MegaBLAST2. Gene Prediction on unmasked sequence
• AUGUSTUS• FGENESH• GeneMark
3. CpG island prediction4. Repeat Masker5. Gene Prediction on masked sequence
• AUGUSTUS• FGENESH• GeneMark
6. BlastX against protein database7. BlastN against EST database8. Pfam9. Blast2Go
MEGABLAST RESULTSExcluding Zea mays Zea mays alone
CPG ISLAND PREDICTION
GENE PREDICTION – RAW SEQUENCE
GeneMark FGENESH AUGUSTUS
Number of Genes 29 23 23
• 13 genes were common between GeneMark, FGENESH, and/or AUGUSTUS
REPEAT MASKER RESULTS
GENE PREDICTION – MASKED SEQUENCE
GeneMark FGENESH AUGUSTUS
Number of Genes 5 2 2
• No genes common between all 3• 1 gene common between FGENESH and
AUGUSTUS
GENE 1 (A, F)• 10175-11176 (138824-139825) on the minus strand• 77% match to hypothetical protein [Zea mays] GenBank:
ACG42783.1 with an e-value of 5E-120• EST evidence : 1 exon with >5 ESTS with >95% identity
• Pfam: no results• Blast2GO: no results
GENE 2 (A, F, G)• 32122-34481 (115519-117878) on minus strand• 52% match to uncharacterized protein LOC100382558 [Zea
mays] with an e-value of 2E-88• 5 exons, EST evidence has evidence for 2:
• Pfam: Seryl-tRNA synthetase N-terminal domain match with E-value of 0.45 (insignificant match)
• Blast2Go: F: Zinc ion binding, C: intracellular
GENE 3 (A, F, G)• 64694 to 71049 (78951-85306) on the minus strand• 100% match to SEY1 with an e-value of 1E-102 : generate and maintain the
structure of the tubular endoplasmic reticulum network, has GTPase activity
• Exons with good evidence
• Pfam: Root hair defective 3 GTP-binding protein (RHD3): regulated cell enlargement, membrane trafficking
• Blast2GO: P:root epidermal cell differentiation, cell tip growth, C: integral to membrane, ER F: hydrolase activity, GTP binding
GENE 4 (G)• 139202 to 139814 on plus strand• 73% match to putative growth-regulating factor 1 [Zea mays]
with an E-value of 1E-7• 3 exons with good ESTs• Pfam: no hit• Blast2Go: no hit
GENE 5 (G, F)• 140856 to 141492 (8508-9144) on minus strand• 91% match to ornithine carbamoyltransferase [Zea mays] with an e-value of 5E-
33• catalyzes the reaction between carbamoyl phosphate (CP) and ornithine (Orn) to
form citrulline (Cit) and phosphate (Pi)• 2 exons with good EST evidence for both• Pfam: no match
• Blast2Go: ornithine carbomyltransferase, EC:2.1.3.0,
F:kinase activity, amino acid binding, carbomyltransferase activity P: phosphorylation, cellular amino acid metabolic process