title: NimbleGen_2005-05-10_Plasmodium_3D7_WG
status: Public on May 18 2009
contact.city: Nijmegen
contact.first: H.G.
contact.last: Stunnenberg
contact.email: h.stunnenberg@ncmls.ru.nl
contact.address: Geert Grooteplein 28
contact.department: Department of Molecular Biology (274)
contact.country: USA
contact.institute: Radboud University
contact.phone: +31-24-3610520
organism: Plasmodium falciparum
description: Annotation in this record based on NCBI Plasmodium falciparum 3D7 strain 2005-05-10
  Initial oligos were selected at 4bp interval in clusters of 10 oligos.  Masking for repetitive elements was done by generating a histogram of 15-mer frequency in the genome and removing oligos with an average 15-mer frequency greater than 100. Oligos were of variable length (45bp to 83bp, median length of 56bp) and the median Tm was 68.7°C. Uniqueness was ascertained by determining the number of exact 45-mer matches of each oligo in the genome. The best oligo from each cluster of 10 was selected based on average 15-mer frequency, uniqueness, Tm, and base pair composition rules. The final set of oligos was arranged using ArrayScribe array design software (NimbleGen Systems Inc.). Arrays were constructed as described previously/
manufacture_protocol: see manufacturer's web site www.nimblegen.com