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Annotating a Scarlet Runner Bean genome fragment put together by shotgun sequencing Scarlet Runner ean Max Bachour.

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Presentation on theme: "Annotating a Scarlet Runner Bean genome fragment put together by shotgun sequencing Scarlet Runner ean Max Bachour."— Presentation transcript:

1 Annotating a Scarlet Runner Bean genome fragment put together by shotgun sequencing Scarlet Runner ean Max Bachour

2 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

3 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.

4 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 Terminal 8577; 8897; Internal 9001; 9131; Internal 9381; 10322; Internal 10616; 10685; Initial 10793; 11395; 603;

5 Fgenesh Predicted three genes. Genes 1 and 3 had no substantial matches Gene 2 once again matched the maturase protein from the soybean.

6 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

7 EST’s Compared to Predicted Genes EST from blasting entire contig and the predicted genes with good matches fit together.

8 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

9 THANK YOU! x THANK YOU! ∞


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