Candidate Oligos for every exon on sanger 22 track
Oligos were chosen for every exon described by the Sanger
annotation of chromosome 22 larger than 70 base pairs. For this
purpose exons are defined to include 3' and 5' UTRs. Oligos
were chosen using the following algorithm:
- Step through each exon at a step size proportional to the
size of the exon examining possible oligos.
- Score each oligos for: Tm difference, distance from 3' end,
secondary structure, and an Affymetrix heuristic.
- Look through candidate probes remembering the maximum
score for each score.
- Each score is then normalized by dividing by the maximum
and then the normalized scores are combined as an average and oligos
are sorted to find the best overall score.
- Oligos with the best combined normalized scores are BLATed
until one is found that has a BLAT score below a given
threshold.
- As oligos are chosen, candidate oligos that overlap those
already chosen are discarded.
- If no scores pass the BLAT score or not enough oligos have been
chosen just pick oligos that have the best combined score.
About the scores:
Please note that all coordinates are relative to the '+' strand
while all oligo sequences are 5'->3'. This means that all sequences
displayed are part of the sense strand. So if the oligo is represented
in the database as being on the '-' strand and starts at 1 and ends at
5 of 'atgcatgc' the '+' sequence of the probe would be 'tgcat' but
that is 3'->5' on the '-' strand so the sequence in the sequence would
be the reverse complement 'atgct'.