The shortest common supersequence problem in a microarray production setting.
BACKGROUND
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 super-sequence problem of several thousand short strings over a four-letter alphabet.


RESULTS
We present a statistical analysis of the basic ALPHABET-LEFTMOST approximation algorithm, and propose several practical heuristics to reduce the length of the super-sequence. Our results show that it is hard to beat ALPHABET-LEFTMOST in the microarray production setting by more than 2 characters, but these savings can improve overall oligo quality by more than four percent.


BACKGROUND
Source code in C may be obtained by contacting the author, or from http://oligos.molgen.mpg.de.
Rahmann
Sven
S
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany. Sven.Rahmann@molgen.mpg.de
D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D015342:DNA Probes / Q000235:genetics*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D015342:DNA Probes; D004247:DNA