ProbeSpec

Introduction
ProbeSpec is a utility for mapping the specificity of all candidate probes for a given sequence (e.g. transcript) against a background containing a large set of sequences (e.g. a transcriptome). Probe specificity is determined by the subsequence in the background that is most similar to its target, the specificity being set as the number of mismatches between the probe and the closest non-specific background sequence. 

ProbeSpec uses an indexed search to limit the number of comparisons between the target and background sequences. The parameter for this search is the seed size used in the index: A large seed means fast results, but certain similarities in the background may be missed. ProbeSpec allows accounting for relative transcript abundance by setting different seed sizes for different scenarios. For example, when searching for a probe to an abundant transcript, scarce background transcript are not likely to be problematic and a long seed may be used for the search. In the reverse situation, an abundant background transcript should be examined thouroughly and a shorter seed should be considered.

Preprepared specificity maps for the entire S. cerevisiae transcriptome are available at this website. An executable for creating maps with different parameters is also available for download, together with a compiled database of the yeast transcriptome including transcript abundance data.

Creation of specificity maps for other organisms is also possible. Preindexing is advised for efficient mapping a large number of sequences. Please contact Doron Lipson for information for other mapping projects. 

Data and Executables for Mapping Probes for Yeast Transcripts
Examples
Probe specificity maps for three yeast transcripts. x-axis denotes position of probe along the transcript sequence, y-axis denotes distance from background. Red markings denote areas of specific probes.
 

GAL1 has some regions of non specificity that are a results of its partial similarity to GAL3

 

GAL2 has very few specific regions since it is very similar to genes from the HXT family (all monosaccharide permeases).

 

GAL4 is completely specific.

Literature
Doron Lipson, Peter Web, Zohar Yakhini (2002) "Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome", WABI '02, 17-21/9/02, Rome.
Authors
ProbeSpec was developed by Doron Lipson and Zohar Yakhini of the Computational Biology Lab, Technion, Israel. 
Comments and questions should be directed at dlipson@cs.technion.ac.il.
Links