Transcript Scarlet Runner

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