SOLICITATION NOTICE
68 -- Single Nucleotide Polymorphism Phylogeny Analysis
- Notice Date
- 2/12/2004
- Notice Type
- Solicitation Notice
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Institute of Allergy & Infectious Diseases/AMOB, 10401 Fernwood Drive, Suite 2NE70, MSC 4811, Bethesda, MD, 20817
- ZIP Code
- 20817
- Solicitation Number
- RML-RFQ-4017
- Response Due
- 2/27/2004
- Archive Date
- 3/13/2004
- Point of Contact
- Julienne Keiser, Purchasing Agent, Phone 406-363-9370, Fax 406-363-9376, - Lynda Kieres, Purchasing Agent, Phone 406-363-9210, Fax 406-363-9288,
- E-Mail Address
-
Jkeiser@niaid.nih.gov, lkieres@niaid.nih.gov
- Small Business Set-Aside
- Total Small Business
- Description
- This notice is a combined synopsis/solicitation for commercial items prepared in accordance with format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only soliciation; quotes being requested & written solicitation will not be issued. This procurement is being issued as a request for quotation. Submit offers on RML-RFQ #4017. Solicitation documents & incorporated provisions & clauses are those in effect through Federal Acquisition Circular 2001-19 dated 1/1/2004. This acquisition will be processed under Simplified Acquisition Procedures (SAP) & is a Small Business Set-Aside. The North American Industry Classification System (NAICS) code for this procurement is 325998 & the small business size is 500. SCHEDULE: The National Institute of Allergy and Infectious Disease (NIAID), Rocky Mountain Laboratories (RML), Laboratory of Human Bacterial Pathogenesis (LHBP), has been charged with performing basic research contributing to the development of diagnostic reagents, therapeutics and vaccines against human bacterial pathogens. The sequencing of bacterial genomes and the interpretation of that genome data is paramount to those diagnostic and vaccine based discoveries. The LHBP now has the need to take completed bacterial genome sequences, sequenced within and external to the LHBP, and perform Single Nucleotide Polymorphism (SNP) phylogeny analysis of them. The Contractor shall generate and provide to LHBP two(2) sets of phylogenetic trees based on synonymous SNPs. The first set of trees shall be a comparison of seven genomes. The second set of trees will be all the genomes in the first set plus one more. This is a 30 day, one time work effort, where the final product will be the production of maps and spreadsheets presenting hyperlinked and interactive data for SNPs for each genome, phylogenetic calculations, and SNP-based phylogenetic trees. The contractor shall keep all RML derived data secure and will not release or maintain any of the data beyond this contract effort. If Internet connectivity is needed in order to perform the work, or transfer deliverables, contractor computers shall be secure and in compliance with RML IT security procedures and policies. LHBP will provide genome data generated by previous or current LHBP research efforts that are needed for construction of the files. Step 1: Identify conserved backbone and variable regions of the Genomes. The contractor shall identify those regions in every genome that vary and correspond to phages, phage regions across the given genomes, and the conserved backbone genome sequence for all of the targeted genomes. Other regions of variation, identified by the contractor, could include remnants of integrated prophages, transposons, or any other hypervariable components. A combination of manual analysis and pre-existing computational tools shall be employed to ensure the information required for the SNP analysis of these genomes is produced accurately and of the highest quality possible. Identification of phage and conserved backbone regions shall take not more than four(4) days. Identification of other hypervariable regions shall take not more than an additional three(3) days. Identification of phage commonality across genomes will take not more than two(2) days. Total not more than nine(9). Deliverables: The contractor shall deliver to RML maps for each genome describing the conserved backbone, phage regions, and other hypervariable regions in each genome. The contractor shall also create a spreadsheet identifying which phage regions are present or absent in the genomes being analyzed. Step 2: Calculate and identify synonymous SNPs. After identification of the conserved backbone and phage regions of the genomes, the contractor shall determine the SNPs in the set of strains and identify those SNPs that are synonymous based on the set of ORFs present in all eight given genomes using existing contractor technology. The contractor shall also analyze the zones conserved in not all eight genomes but only in related genomes and identify the synonymous substitutions in them. Identification of SNPs shall take not more than five(5) days; analysis of partially conserved zones shall take an additional not more than three(3)days. Total not more than eight (8)days Deliverables: The contractor shall deliver to RML an Excel spreadsheet containing all primary information about each SNP and its position relative to both the contig it is located on, and the gene it is relevant to, along with links into an ERGO database that will display sequence alignments. The contractor shall also generate a plot similar to the one published in Garnier, et al., (2003) PNAS 100: 7877, which shows the number of SNPs per ORF. Step 3: The contractor shall build a distance matrix and construct a robust phylogenetic tree. The contractor shall examine the synonymous SNPs in the context of orthologous groups of genes, which shall make it possible to calculate a distance matrix and to construct a robust phylogenetic tree. Two phylogenetic trees shall be constructed for the given set of genomes. The first tree shall be based upon only the conserved backbone of the genomes without phage regions removed from the data. The second tree shall be based on both the conserved backbone and the phage insertions. This latter tree shall analyze the full genome sequences of the genomes. To ensure robustness of the generated trees, a number of matrices and trees shall be constructed for both data sets, based on different selections of genes. The generated trees will be examined for isomorphism. If the significant differences are encountered, the contractor shall attempt to identify the causes for them. To ensure statistical robustness of the generated trees the contractor shall perform bootstrap testing, via the PHYLIP package or a comparable package .Construction of initial set of trees, verification of isomorphism ? not more than five(5) days. Analysis of differences ? not more than five(5) days. Construction of the final trees: not more than one(1) day. Verification of the robustness of trees ? not more than two(2) days. Total not more than fourteen(1)4 days. Deliverables: The contractor shall deliver to RML all generated distance matrices and trees in Newick format. Step 4: The contractor shall create publication quality tree images. A publication quality tree image shall be generated using a publicly available software package such as FORESTER. The composition of this image shall be determined between contractor and RML to meet the needs of the RML publication. Duration, 5 days. Deliverables: The contractor shall deliver to RML, publication quality images of the phylogenetic trees generated based on the conserved backbones of the genomes and the conserved backbone plus phage insertions. FOB Point shall be Destination, Hamilton, MT. Delivery as annotated above. The following FAR provisions & clauses apply to this acquisition: As of October 1, 2003, All Vendor/Contractor (s) must be registered in the Central Contractor Registration System, in order to do business with the Federal Government. Lack of registration in the CCR will make an offeror ineligible for award. http://www.ccr.gov. FAR 52.227-14 Rights And Data Clause; FAR52.212-1 Instructions to Offerors-Commercial; FAR52.212-2 Evaluation-Commercial Items; FAR52.212-4 Contract Terms & Conditions Commercial Items; FAR52.212-5 Contract terms & Conditions Required to Implement Statues or Executive Orders-Commercial Items; FAR52.246-2 Inspection of Supplies-Fixed Price. Offerors must include along with their offer a completed copy of the provisions at FAR52.212-3 Offerors Representations & Certifications Commercial Items. Award will be based on capability to meet above stated salient characteristics, including technical, delivery, price & past performance. Offers may be mailed or faxed to POC indicated above(Fax 406-363-9376). Offers must be submitted not later than 4:30 PM(MDST), _2/27/04_.Copies of the above-referenced clauses are available upon request, either by telephone or fax. All responsible sources may submit an offer that will be considered by this Agency.
- Place of Performance
- Address: Rocky Mountain Laboratories, 903 S. 4th Street, Hamilton, MT
- Zip Code: 59840
- Country: USA
- Zip Code: 59840
- Record
- SN00521356-W 20040214/040212212110 (fbodaily.com)
- Source
-
FedBizOpps.gov Link to This Notice
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