1. Functional Annotation Final Results

2. Annotations : Coding Regions

3. Pipeline: Coding Regions

4. Structure annotation Lipo-Protein - LipoP Signal-peptide - SignalP
Transmembrane proteins-TMHMM
Protein domain identification-Interproscan and CD search

5. LipoP

6. Interproscan and CD search
The results for the two softwares is similar but we used CD search because the cas genes were highly annotated by CDD database which is not included Interproscan.

7. Interproscan and CD search
The results for the two softwares is similar but we used CD search because the cas genes were highly annotated by CDD which is not included in Interproscan.

8. Function annotation Specific Annotation : Virulence Factors-VFDB
Antibiotic resistance proteins- CARD
Overall Annotation :
Uniprot
Refseq

9. VFDB and CARD results
This table shows the number of virulent and antibiotic resistant genes annotated by each database, these results show that the virulent genes are mostly conserved across the serogroups.

10. Gene Ontology
The table shows the classification of the gene ontologies for our samples

11. Pathway annotation MetaCyc UniPathway
Kobas-KEGG Orthologous Based Annotations

12. Pathway Results Annotated Genes
Kegg orthology based annotation gave us the more annotations than the other two databases, however we wanted to include experimental database too from MetaCyc. MetaCyc is available through Interpro.

13. Pathway Results
Total Number of Genes
Annotated genes

14. Gene Naming E-value<10e-50 Alignment length>100 Coverage>60%
Absolute Function
All 3 criteria fulfilled
E-value<10e-50
Alignment length>100
Coverage>60%
Conserved Hypothetical Function
All criteria meet with”hypothetical” term
Hypothetical Proteins
No criteria fulfilled

15. Number of Genes as per naming

16. Total Annotated Genes vs Total number of Genes Predicted

17. 1827
834
640
355

18. Annotations : Non - Coding Regions

20. RNAs and CRISPRs
This table shows the number of RNA elements found in each sample. CRISPRs were fairly difficult to annotate because each software (minced/Rfam/CRISPR finder) had their own algorithm to identify crisprs leading to inconsistency with the results obtained. We concluded to use CRISPR finder through CRISPR DB.

21. Deliverables Completely annotated gff files uploaded to the server.
The annotations included the following information:
id=<gene ID>;Name=<gene symbol>;signature=<Gene name>;GO=<GO ID>;Interpro=<Interpro ID>;KEGG=<KEGG ID>;UniPathway=<UniPathway ID>;MetaCyc=<MetaCyc ID>;TMHMM=<Yes/NO>;Coils=<Yes/No>;SignalP=<Yes/No>;LipoP=<Yes/No>;comment=< LOCATION;CATALYTIC ACTIVITY;SIMILARITY;PATHWAY>

22. Questions???