title: Lactococcus lactis pangenome 385K short oligo array
status: Public on Dec 31 2008
contact.city: Nijmegen
contact.first: Jumamurat
contact.last: Bayjanov
contact.address: Geert-Groteplein
contact.country: Netherlands
contact.institute: CMBI
organism: Lactococcus lactis
description: All genomic, plasmid and single gene or operon DNA sequences (1988 sequences in July 2005, constituting 10.7 Mb) of L. lactis were collected from the NCBI CoreNucleotide database and were deposited in a local database. This included complete genome sequences of L. lactis strain IL1403 (2.35 Mb, accession number AE005176) and fragments of the genome of strain SK11 (2.43 Mb, Genbank record GI:62464763). Additionally, draft genome sequences consisting of 547 contigs (2.3 Mb) of L. lactis ssp. lactis strain KF147 (NIZOB2230) and 961 contigs (2.6 Mb) of L. lactis ssp. lactis KF282 (NIZOB2244W) were added to this database. Redundant stretches of DNA were removed from the database, where a stretch of DNA was defined as redundant if it differed from another piece of DNA by at most 2 nucleotides over a window of 100 nucleotides. For the remaining non-redundant 7 Mb of DNA, a 32-mer tiling design was defined by starting an oligomer approximately every 19 nucleotides, resulting in a total of 386,298 probes. We also designed 3181 random probes with their sequence absent in the non-redundant 7 Mb of DNA and they were randomly located on the array.
  Probes target mainly L. lactis ssp. lactis IL1403 public genome and then incomplete genome of L. lactis ssp. cremoris SK11 (now it is completed). Recently, closely related genome of strain L. lactis ssp. cremoris MG1363 has been published. All these 3 genomes are publicly available at NCBI databases.
  Since there is no reference strain the probes target DNA from different strains, hence, there is no positions file (*.pos). The .ndf file is linked below as a supplementary file.
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