(Submitter supplied) The 16S rRNA gene probe design for the microarray was as follows: 1) database searches in Greengenes (http://greengenes.lbl.gov) for 16S rRNA gene sequences with keywords "Arctic," "Antarctic," "Polar," "Cold," "Psychro" (2891 sequences retrieved, performed on April 15th, 2008); 2) clustering of the database sequences together with 16S rRNA gene sequences from strains isolated in our lab in previous studies of polar environments using Blastclust (NCBI, Bethesda, MD); 3) design of five 25-mer probes for each of the 99%-similarity clusters having 3 or more representatives using OligoPicker (32); 4) elimination of probes having a ΔG >-3 kJ; 5) BLAST comparison of the central 17 nucleotides of each probe against all the original sequences; 6) selection, for each cluster, of the probe that showed less significant hits to sequences outside the cluster and most significant hits within the cluster.
more...- Organism:
- Bacteria; Archaea
- 5 Series
- 115 Samples
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