de.mpg.escidoc.pubman.appbase.FacesBean
Deutsch
 
Hilfe Wegweiser Impressum Kontakt Einloggen
  DetailsucheBrowse

Datensatz

DATENSATZ AKTIONENEXPORT

Freigegeben

Zeitschriftenartikel

The shortest common supersequence problem in a microarray production setting

MPG-Autoren
http://pubman.mpdl.mpg.de/cone/persons/resource/persons50480

Rahmann,  Sven
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

Externe Ressourcen
Es sind keine Externen Ressourcen verfügbar
Volltexte (frei zugänglich)
Es sind keine frei zugänglichen Volltexte verfügbar
Ergänzendes Material (frei zugänglich)
Es sind keine frei zugänglichen Ergänzenden Materialien verfügbar
Zitation

Rahmann, S. (2003). The shortest common supersequence problem in a microarray production setting. Proceedings of the European Conference on Computational Biology (ECCB 2003), ii156-ii161. doi:10.1093/bioinformatics/btg1073.


Zitierlink: http://hdl.handle.net/11858/00-001M-0000-0010-89BE-E
Zusammenfassung
Motivation: During microarray production, several thousands of oligonucleotides (short DNA sequences) are synthesized in parallel, one nucleotide at a time. We are interested in finding the shortest possible nucleotide deposition sequence to synthesize all oligos in order to reduce production time and increase oligo quality. Thus we study the shortest common supersequence problem of several thousand short strings over a four-letter alphabet. Results: We present a statistical analysis of the basic ALPHABET-LEFTMOSTapproximation algorithm, and propose several practical heuristics to reduce the length of the supersequence. Our results show that it is hard to beat ALPHABET-LEFTMOSTin the microarray production setting by more than 2 characters, but these savings can improve overall oligo quality by more than four percent.