SRB Genome

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SRB Genome Assembly and Analysis From 454
Sequences
HC70AL S09 04-21-09 Brandon Le Min Chen
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Genome Sequence Analysis - Step Two Determine
Open Reading Frame
Assembled DNA Sequence
CONTIG 2
CONTIG 3
CONTIG 1
CONTIG 5
CONTIG 4
GENE 1
GENE 2
Identify ORF
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SRB Genome Information
Genome Information Genome Information
Genome Size 670 Mba
Number of Chromosomes 11
Ploidy 2n
a. Broughton et al. (2003) Beans (Phaseolus spp.) model food legumesPlant and Soil. a. Broughton et al. (2003) Beans (Phaseolus spp.) model food legumesPlant and Soil.
Sequencing Information Sequencing Information
of Sequences 802,779
Total of Sequenced Bases 291,416,275
Avg. Read Length 363
Assembly Information Assembly Information
of Contigs 81,888
of Reads in Contigs 415,891
Largest Contig Size 20,991
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GENSCAN
http//genes.mit.edu/GENSCAN.html
1. Select Organism (Vertebrate, Arabidopsis,
Maize)
2. Print Options (Predicted peptides only)
(Predicted CDS and peptides)
3. Copy and Paste Sequence
4. Click Run GENSCAN
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GENSCAN Output
Predicted Genes
Gene Structure
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FGENESH
http//linux1.softberry.com/berry.phtml?topicfgen
eshgroupprogramssubgroupgfind
1. Copy and Paste Sequence
2. Organism (Select Dicot plants(Arabidopsis)
(Medicago (legume plant))
3. Click SEARCH
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FGENESH Output
Predicted Coding Sequence
Predicted Peptide
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GENEMARK.HMM Output
Predicted Peptide
Predicted Peptide
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REPEAT MASKER
http//www.repeatmasker.org
1. Copy and Paste Sequence
2. DNA Source (Arabidopsis thaliana)
3. Submit Sequence
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REPEAT MASKER OUTPUT
1. Number of Retroelements
2. Number of DNA Transposons
3. Simple Repeats
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