Figure 2: The distribution of Saccharomyces cerevisiae sequences. Computed minimum free energy is on the x-axis, z score is on the y-axis. Black lines denote the mean values and gray lines define sequence windows that are one and two standard deviations less than mean. Clicking on any region links to the closest -1 PRF signals with respect to MFE and z score.

Mentions: Researchers can access data in the PRFdb through four means: (i) Search (Figure 1) provides a way to query a gene of interest using the specific gene name or description from the yeast genome project or mammalian gene collection. The search interface also provides a means to use BLAST to search for genes in the PRFdb similar to a query sequence. ii) Distribution (Figure 2) enables browsing for sequences containing statistically significant putative -1 PRF signals through a graphical representation of computed minimum free energies with respect to randomized z scores for all sequence windows. It is also possible to limit this distribution to sequences that are preceded by a specific slippery site. iii) Filter prints sequences from a given genome that meet specific criteria including: species, pseudoknotted sequence, sequences with a specific number of base pairs and/or MFE. iv) Download provides a format suitable for parsing all sequences of a given genome/sequence dataset.