1. Cuong Nguyen, Deng Xin, Dongmei, Zheng Wang
Genome Annotation
Group 3
Cuong Nguyen, Deng Xin, Dongmei, Zheng Wang
1) Introduction
2) Methodology
3) Selection of Tools
4) Role of Group Members
5) Project Time Frame

2. Introduction Genome annotation:
- Identifying useful elements in the genome,
- And providing biological information to these elements.
- Manual curation
- Automated annotation
In our genome annotation project, we use automated method to annotate elements in the genome, by applying both homology-based and ab inito approaches.

3. Methodology Genome sequence Genome browser search NCBI, ENSEMBLE … yes
Contains known or predicted genes no no
Flowchart: Steps in our Annotation Project
Pseudogene finder
(PPfinder)
Repeat mask sequence (RepeatMasker)
Homology search
(FGENESH, BLAST, EST, cDNA..)
Generate model for training
Visual integration
of the results
(CGView, …)
Evaluation
Ab inito prediction
(FGENESB, Glimmer, GOana …)

4. Tools - Repeat sequences: RepeatMasker - Pseudo-genes: PPfinder
- Homology based approaches: FGENESH, GOana, SGP2, Exonerate
- Ab Inito approaches: FGENESB; Glimmer, GeneMark, BProt, GrailEPX
- Visualization: CGView, Apollo, Softberry

5. Project team member roles:
Name
Role
Tasks
Cuong Nguyen
Coordinator
- Working together with the project team members
- Presentation, final report writing and submission
Zheng Wang
Member
Installation and testing of the tools and integration of the results generated, visualization
Deng Xin
Homology-based approaches
Dong Mei
Ab Inito approaches

6. Project Time frame: Activities Oct. 02-> Oct. 07-> Oct. 09->
Planning and tool selection
Installation
Testing and implementation
Evaluation and Validation
Report writing and submission

7. Homology based approach --FGENESH
Introduction
FGENESH has both program version and web-site
It can do Hidden Markov Model-based Gene prediction
We choose website---more convenient

8. Homology based approach --FGENESH

9. Homology based approach --FGENESH
How to use it
Paste your assigned genomic sequence into the sequence window or load the FASTA file
select the most similar organism to assist in gene prediction
Select the following "advanced options" from the list below: - print mRNA sequences for predicted genes - print exon sequences for predicted genes
Click the "Search" button

10. Homology based approach --FGENESH
output

11. Ab inito approach GLIMMER
GLIMMER (ver. 3.02; iterated) predictions:
orfID start end frame score
>scf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf
orf

12. GeneMark Parse predicted by GeneMark.hmm 2.4
GeneMark.hmm PROKARYOTIC (Version 2.6r)
Model organism: Escherichia_coli_K12
Tue Oct 6 20:00:
Predicted genes
Gene Strand LeftEnd RightEnd Gene Class
# Length
<

14. Fgenesb Prediction of potential genes in microbial genomes
Time: Tue Jan 1 00:00:
Seq name: test sequence
Length of sequence bp
Number of predicted genes - 25
Number of transcription units - 18, operons - 3
N Tu/Op Conserved S Start End Score
pairs(N/Pv)
Op CDS
Op CDS
Tu CDS
Tu CDS
Tu CDS
Op CDS

15. CGView – Circular Genome Viewer
Java-based tool
Run from web browser, Java-applet
Circular genomes
Integrated into bacterial genome annotation pipeline, and generates web content for data visualization
Support many formats, such as XML, tab delimited file, or an NCBI PTT file
Convenient to use with FgenesB 15

16. CGView – Circular Genome Viewer16

17. 17

18. Thank You! 18