1. SRB Genome Assembly and Analysis From 454 Sequences HC70AL S09 04-21-09 Brandon Le & Min Chen

2. Shotgun Genome Sequencing original DNA 454 Sequencing Sequence Analysis Begins!!! fragmented DNA REPEAT 1

3. Genome Sequence Analysis - Step Two Determine Open Reading Frame CONTIG 1 CONTIG 3 CONTIG 5 CONTIG 2 CONTIG 4 Assembled DNA Sequence GENE 1 GENE 2 Identify ORF

4. SRB Genome Information Genome Information Genome Size670 Mb a Number of Chromosomes11 Ploidy2n a. Broughton et al. (2003) Beans (Phaseolus spp.) – model food legumesPlant and Soil. Sequencing Information # of Sequences802,779 Total # of Sequenced Bases 291,416,275 Avg. Read Length363 Assembly Information # of Contigs81,888 # of Reads in Contigs 415,891 Largest Contig Size 20,991

5. GENSCAN http://genes.mit.edu/GENSCAN.html 11. Select Organism (Vertebrate, Arabidopsis, Maize) 33. Copy and Paste Sequence 22. Print Options (Predicted peptides only) (Predicted CDS and peptides) 44. Click Run GENSCAN

6. GENSCAN Output Predicted Genes Gene Structure

7. FGENESH 11. Copy and Paste Sequence 22. Organism (Select Dicot plants(Arabidopsis) (Medicago (legume plant)) 33. Click SEARCH http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind

8. FGENESH Output Predicted Peptide Predicted Coding Sequence

9. GENEMARK.HMM 11. Copy and Paste Sequence 22. Species (A. thaliana ES-3.0) (M. truncatula ES-3.0) 33. Check Box Check Generate Postscript graphics Check Generate PDF graphics Translate predicted genes into protein http://exon.gatech.edu/eukhmm.cgi 44. Click Start GeneMark.hmm

10. GENEMARK.HMM Output Predicted Peptide

11. REPEAT MASKER 11. Copy and Paste Sequence 22. DNA Source (Arabidopsis thaliana) http://www.repeatmasker.org 33. Submit Sequence

12. REPEAT MASKER OUTPUT 11. Number of Retroelements 22. Number of DNA Transposons 33. Simple Repeats

13. PLANT REPEAT DATABASE 22. Copy and Paste Sequence 33. Select BLAST Database (Brassicaceae Repeats) (Fabaceae Repeats) http://plantrepeats.plantbiology.msu.edu/search.html 44. Submit BLAST Search 11. Select BLAST program (blastn) (blastp) (blastx)

14. BLAST OUTPUT PLANT REPEAT DATABASE OUTPUT Top BLAST HIT Sequence Alignment