title: UF Nimblegen Populus trichocarpa Array
status: Public on Sep 06 2008
contact.city: Gainesville
contact.first: Matias
contact.last: Kirst
contact.email: mkirst@ufl.edu
contact.state: FL
contact.country: USA
contact.institute: University of Florida
contact.phone: 352-8460900
organism: Populus trichocarpa
description: Populus trichocarpa 'Nisqually-1'
manufacture_protocol: The 60-mer oligonucleotide probes were designed based on v.1.1 of the P. trichocarpa genome sequence and NimbleGen standard procedures. Briefly, 24-mers tiling each possible 60-mer oligonucleotide were analyzed for sequence similarity to other regions of the genome. Each perfect match of a 24-mer to a segment of the genome was given a score of 1. Because 37 24-mers are required to fully tile a 60-mer, the best possible uniqueness score for a 60-mer probe is 37. In addition, a weighted similarity score that favors probe uniqueness at the core 12 nucleotides was used. A minimum of three unique positions in the core 12 nucleotides were required for the probe to be considered.  Resulting oligonucleotides were subsequently subjected to additional filtering steps that considered self-complementarities, GC/AT content, and homopolymer runs.