Computational Design of Oligonucleotide Bar Code Tag Sequences
Molecular barcoding is also a promising technology for high-throughput assays in many areas. Distinct barcode tags are attached to biological units (e.g., open reading frames in the yeast deletion project), and then the abundance of tags in a sample is quantified by hybridization to a DNA microarray of tag complements. Known existing tag sets consist of fewer than 20,000 tags. This is enough for current experiments, but not for possible future applications such as using molecular inversion probes to assay all known human splice junctions in mRNA samples. We have developed computational methods for designing bar code sequences for sets with up to two million tags.
Personnel
Zhi Li
Ted Jones
Ron Davis
Impact/Significance
and computational issues helps guide the design of large tag sets.
Our framework is flexible and allows new design criteria to be added in a modular fashion.
Accomplishments
Sets of a few thousand tag sequences can be created in minutes.
We have created sets with over 2 million tag sequences having properties similar to those of the yeast deletion tag set.
Computational issues need not become a bottleneck in developing new technologies that use bar codes.
genome Technology Center 
Molecular barcoding is also a promising technology for high-throughput assays in many areas. Distinct barcode tags are attached to biological units (e.g., open reading frames in the yeast deletion project), and then the abundance of tags in a sample is quantified by hybridization to a DNA microarray of tag complements. Known existing tag sets consist of fewer than 20,000 tags. This is enough for current experiments, but not for possible future applications such as using molecular inversion probes to assay all known human splice junctions in mRNA samples. We have developed computational methods for designing bar code sequences for sets with up to two million tags.