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

THANK YOU! x

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

∞

THANK YOU!

THANK YOU!

THANK YOU!THANK YOU!

THANK YOU!

THANK YOU!THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!THANK YOU!

THANK YOU!

THANK YOU!THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!

THANK YOU!