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DRAFT ENVIRONMENTAL ORGANISMS PANEL, VERSION
5
2.2
Bioinformatics Analyses
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In silico
screening shall be performed on all nucleic acid signature sequences used in the assay (e.g.,
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primers, probes, amplicons, etc.) to demonstrate specificity to the target biological threat agent.
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In silico
results are suggestive of potential performance issues, so will guide necessary additions to the
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wet screening panels.
In silico
identification of potential cross‐reactions (false positives) or non‐
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verifications (false negatives) would require the affected organism/strain be included in the exclusivity
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or inclusivity panels, respectively, if the strains are available.
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A method developer‐selected tool to carry out the bioinformatics evaluation should be able to predict
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hybridization events between signature components and a sequence in a database including available
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genomic sequence data, databases and/or published documents describing the genetic sequences found
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in soils that are representative of the regions of operation. The selected tool should be able to identify
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predicted hybridization events based on platform annealing temperatures, thus ensuring an accurate
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degree of allowed mismatch is incorporated into predictions. The program should detect possible
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amplicons from any selected database of sequences.
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Potential tools for in silico screening of nucleic acid sequences include:
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http://sourceforge.net/projects/simulatepcr/files/?source=navbar
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o
This program will find all possible amplicons and real time fluorescing events from any
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selected database of sequences.
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NCBI tools
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The method developer submission should include:
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Description of sequence databases used in the
in silico
analysis
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Description of conditions used for
in silico
analysis
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o
Stringency of
in silico
analysis must match bench hybridization conditions
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Description of the tool(s) used for bioinformatics evaluation
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o
Data demonstrating the selected tool(s) successfully predicts specificity that has been
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confirmed by wet‐lab testing on designated isolates
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These data can be generated retrospectively using published assays
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List of additional organisms and/or strains to be added to the inclusivity (Annex II) or exclusivity
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(Annex III) panels based on the bioinformatics evaluation
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