An algorithm and program for finding sequence specific oligonucleotide probes for species identification.
BACKGROUND
The identification of species or species groups with specific oligo-nucleotides as molecular signatures is becoming increasingly popular for bacterial samples. However, it shows also great promise for other small organisms that are taxonomically difficult to tract.


RESULTS
We have devised here an algorithm that aims to find the optimal probes for any given set of sequences. The program requires only a crude alignment of these sequences as input and is optimized for performance to deal also with very large datasets. The algorithm is designed such that the position of mismatches in the probes influences the selection and makes provision of single nucleotide outloops. Program implementations are available for Linux and Windows.
Pozhitkov
Alexander E
AE
University of Cologne, Institute of Genetics, AG Tautz; Weyertal 121, D-50931 Cologne, Germany. alex.pozhitkov@uni-koeln.de
Tautz
Diethard
D
D000465:Algorithms; D019295:Computational Biology / Q000706:statistics & numerical data; D020118:Cupriavidus necator / Q000235:genetics; D030541:Databases, Genetic; D020563:Gammaproteobacteria / Q000235:genetics; D015345:Oligonucleotide Probes / Q000235:genetics*; D012329:RNA, Bacterial / Q000235:genetics*; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D012985:Software Design; D013045:Species Specificity; D016944:Sulfolobus / Q000235:genetics; D020124:Thermotoga maritima / Q000235:genetics; D014208:Treponema / Q000235:genetics
D015345:Oligonucleotide Probes; D012329:RNA, Bacterial; D012337:RNA, Ribosomal, 18S; D012339:RNA, Ribosomal, 28S