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Annotating a Scarlet Runner Bean genome
fragment put together by shotgun sequencing
Scarlet Runner ean
Max Bachour
Predicting Genes
• Web based programs can predict the genes in a sequence.
• These predicted genes are then checked against the NCBI database to see if they match any known gene or protein.
• Three gene predicting programs are:– Genescan– FGenesh– GeneMark
Genscan
• Genscan predicts three genes, the first two don’t match anything substantial.
• The third gene however showed a large number of matches when the protein sequence was blasted.
• A number of strong matches with a “maturase related” protein were found; the most notable one coming from a soybean, a close relative to the SRB.
GeneMark• Genemark predicted 20 genes. Only gene 10 had a substantial match against protein data base.
• Again protein predicted from gene 10 matched with maturase. In addition there was a match to an unnamed protein in grapes.
10 5 - Terminal 8577; 8897; 321 10 4 - Internal 9001; 9131; 131 10 3 - Internal 9381; 10322; 942 10 2 - Internal 10616; 10685; 70 10 1 - Initial 10793; 11395; 603;
Fgenesh
• Predicted three genes. Genes 1 and 3 had no substantial matches
• Gene 2 once again matched the maturase protein from the soybean.
Expressed Sequence Tags (EST’s)
EST’s help us further confirm the accuracy of the predicted gene
Many records of a sequence being expressed makes being a gene more likely
Goldberg Lab EST
EST’s Compared to Predicted Genes
EST from blasting entire contig and the predicted genes with good matches fit together.
Conclusion
• No significant repeats• Maturase gene has overwhelming evidence
that it is in fact a real gene.• Error Value low and high EST match• Sequence again• Examine more contigs
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