An algorithm for the determination and quantification of components of nucleic acid mixtures based on single sequencing reactions.
BACKGROUND
Determination and quantification of nucleic acid components in a mixture is usually accomplished by microarray approaches, where the mixtures are hybridized against specific probes. As an alternative, we propose here that a single sequencing reaction from a mixture of nucleic acids holds enough information to potentially distinguish the different components, provided it is known which components can occur in the mixture.


RESULTS
We describe an algorithm that is based on a set of linear equations which can be solved when the sequencing profiles of the individual components are known and when the number of sequenced nucleotides is larger than the number of components in the mixture. We have implemented the procedure for one type of sequencing approach, pyrosequencing, which produces a stepwise output of peaks that is particularly suitable for the procedure. As an example we use signature sequences from ribosomal RNA to distinguish and quantify several different species in a mixture. Using simulations, we show that the procedure may also be applicable for dideoxy sequencing on capillary sequencers, requiring only some instrument specific adaptations of protocols and software.


CONCLUSIONS
The parallel sequencing approach described here may become a simple and cheap alternative to microarray experiments which aim at routine re-determination and quantification of known nucleic acid components from environmental samples or tissue samples.
Pozhitkov
Alexander
A
Institut für Genetik, der Universität zu Köln, Zülpicherstrasse 47, 50674 Köln, Germany. pozhit@u.washington.edu
Stemshorn
Kathryn
K
Tautz
Diethard
D
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D015342:DNA Probes; D020869:Gene Expression Profiling; D007090:Image Interpretation, Computer-Assisted; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D009696:Nucleic Acids / Q000737:chemistry*; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein; D012689:Sequence Homology, Nucleic Acid; D012984:Software
D015342:DNA Probes; D009696:Nucleic Acids; D015345:Oligonucleotide Probes; D004247:DNA