Check Oligonucleotides against Database

In this step all the oligos identified so far are screened for their ability to target the identified target group to the exclusion of all other records.  Potentially useful oligos will be those which target the most records within the defined target group whilst targeting the least number of records outside of this target group.

1) On the main panel, click ' Check Oligonucleotides against Database'.  A dialog box is displayed , showing the database records (top left panel), with target records marked; a list of those target records used to design the oligonucleotides to be screened (top right table); and a summary of the number of oligonucleotides identified previously. 



2) Select the maximum number of acceptable non-target hits you want your oligonucleotide to target. 

3) Click ' Search Database Records' to start analysis.  The speed of this step will depend on the number of oligos to be screened, the size of the database and the maximum number of non-targets allowed.
Each oligo is screened against each database record and the number of matches (hits) recorded - oligos which exceed the maximum number of non-target records hit are discarded as the analysis proceeds, as indicated by the number display near the bottom of the dialog.  


As more records are excluded, the program will speed up, so the estimation of the time remaining, appearing at the bottom of the dialog box, will be somewhat conservative initially.  The search can be aborted at any time by clicking the 'Abort search' button.

4) Analysis complete, the successful oligos are listed in the main table.  Oligos are listed as 5' - 3' sense sequences, colour coded (, , ) according to their success in terms of targeting the specified target group. 


Alongside each oligo is:
Click on column header to sort any colum in ascending numerical (or alphabetical for oligos) order.

Any oligonucleotide listed can be explored further by double clicking on its sequence.  This opens a further dialog box displaying the selected oligonucleotide and the database, with targets marked.