Transcript ch15-figs.ppt

Raw data parser extracts coding
regions, checks ORFs, etc., from
a complete genome downloaded
in either EMBL or GenBank format
MySQL
•All contig seqs
•All cDNAs
•All exons
Probe producer computes oligos
of a given length for each ORF in
the genome, subject to specified
criteria, such as G+C content,
secondary structure formation,
cross-homolog, etc.
Optimal probe selector chooses
optimal probes from all computed
probe candidates of each ORF wrt
some rules. E.g., for eukaryotes,
probes selected are as close to
3’ end as possible.
1. Create objects from the database
2. Select one CDS, e.g., pick one segment from 3’ end
n
3. Does segment satisfy constraints?
y
4. Compare to all the other segments from all the other CDSs
n
5. Is minimum Hamming distance > threshold?
y
6. Insert into Probes Table in the database
n
7. Sufficient number of probes found or no more candidate?
y
8. Stop