SOLICITATION NOTICE
68 -- Genomic Sequencing
- Notice Date
- 8/26/2004
- Notice Type
- Solicitation Notice
- NAICS
- 325414
— Biological Product (except Diagnostic) Manufacturing
- 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
- Reference-Number-RML-RFQ-4038
- Response Due
- 9/10/2004
- Archive Date
- 9/25/2004
- Point of Contact
- Jenny Lovitt, Purchasing Agent, Phone 406-363-9489, Fax 406-363-9288, - Rebecca Guenthner, Chief Contracting Officer, Phone 301-402-2284, Fax 301-480-3695,
- E-Mail Address
-
jlovitt@niaid.nih.gov, rguenthner@niaid.nih.gov
- Description
- This notice is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested and a written solicitation will not be issued. This procurement is being issued as a request for quotation. Submit offers on RML-RFQ-4038. The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2001-24 dated 06/18/04. This acquisition will be processed under Simplified Acquisition Procedures (SAP) and is not a Total Small Business Set-Aside. The North American Industry Classification System (NAICS) code for this procurement is 325414 and the small business size is 500 employees. The Rocky Mountain Laboratories, Laboratory of Intracellular Parasites requires the determination of the chemical sequence of the DNA of a two bacterial pathogen genomes, each estimated to be 2,040,000 bases in size, which will include sequencing, assembly and professionally annotating a genome to total completion. Genome sequencing involves two phases. Phase I:1)The Contractor shall construct two libraries for shotgun sequencing, one library shall contain 2-3 kb inserts, one library shall contain 10 kb inserts, libraries shall be constructed by random, mechanical shearing, libraries shall be non-amplified, quality control tested for ligation, size distribution of fragments, clone integrity and quality of paired-end sequencing; 2)7X continuous shotgun sequencing via both ends of clones from both libraries based on the predicted size of the genome from the first 2000 reads with no other projects or sequencing efforts interrupting or intermingling with the continuous shotgun genome effort, clones shall be picked for template purification and freezer storage by robotic colony picking robots, templates shall be isolated by alkaline lysis and sequenced by PCR using the di-deoxy method of Sanger and vector-specific primers, no less than two rounds of auto finishing shall be performed; 3)assembly using publicly available assembler software, 4)closure to single ungapped genome by PCR and primer walking, using large and small insert library templates, total finished sequence quality at Q40 or higher, or no more than 1 base error per 10,000 bases of sequence throughout entire gnome sequence. Duration of Phase I shall be no more than 5 months from receipt of purified genomic DNA from the Government. Phase II:1)Analysis and annotation of the complete genome sequence shall be performed by computer driven and manual analysis techniques to find all open reading frames (ORFs) and relate ORFs to known proteins by similarity searches against databases. The first round automated analysis for ORF calling and functional analysis shall be performed using software pre-approved by the Project Officer. The Contractor shall perform a second round of manual analysis for annotation purposes focusing on related annotated genomes for comparison. The Contractor shall perform an analysis of gene conservation and identify horizontally transferred regions based on insertion/deletion events or GC skew profiles. The Contractor shall determine potential promoter and ribosome binding sets, frame shifts/point mutations, identify untranslated regions (tRNAs, rRNAs, insertions sequences), perform comparative analysis with previously sequenced isolates and characterize the genetic, metabolic and pathogenic potential of the new genome. Duration of Phase II shall be no more than 7 months from the completion of Phase I. Deliverables shall be: Trace data for all primer-walking/finishing reactions in SCF format; shall be available for ftp download. A preliminary draft of the single contig/chromosome assembled where the total genome is at Q40 or higher (no more than one error per 10,000 bases) ; contigs in flat file format; gene annotation and pathway information (EMBL format); a list of unique and conserved ORFs and DNAs for the genome, as compared to all existing related genomes; final genome annotation and pathway identification; and a final list of unique and conserved ORFS and DNAs for the new genome compared to all other closely related publicly available genomes; all files shall be provided in flat file format on CD. Internet connectivity to Contractor?s graphics-based genome data analysis and data interpretation interface shall be provided. The Contractor?s Project Director shall provide status/progress reports to the RML Project Officer on a weekly basis by e-mail. All work shall be performed with controlled SOPs that include detailed instructions for each laboratory protocol software application or use, and maintenance of equipment. The Contractor shall strictly adhere to Quality Control measures such that contamination from other organism DNAs shall not occur. The Contractor shall perform proper sterilization and aseptic techniques and accurate data tracking and inventory. The Contractor shall use appropriate robotics for colony picking and sample preparations in 384 well blocks. High plasmid concentration and purity along with a robust sample tracking system shall be in place to aid di-deoxy sequencing in 384 well plates on 3700 or 3730 ABI sequencers. FOB Point shall be Destination, Hamilton, MT. Delivery location is Rocky Mountain Laboratories, 903 S. 4th Street, Hamilton, MT. The following FAR provisions and clauses apply to this acquisition: 52.212-1 Instructions to Offerors-Commercial Items; FAR 52.212-2 Evaluation-Commercial Items; FAR 52-212-4 Contract Terms and Conditions-Commercial Items; FAR 52-212.5 Contract Terms and Conditions Required to Implement Statues or Executive Orders-Commercial Items; FAR 52.242-2 Production Progress Reports; FAR52.244-2 Subcontracts; FAR52.246-2 Inspection of Supplies-Fixed Price; FAR 52.227-14 Rights in Data-General, HHSAR 352.224-70 (b) (f) Confidentiality Clause. Offerors must include with their offer a completed copy of the provisions at FAR 52.212-3 Offerors Representations and Certifications-Commercial Items. Award will be based on: The capability to meet the above stated salient characteristics, delivery, past performance and price. Offers may be mailed or faxed to the POC indicated above (Fax - 406-363-9489). Offers must be submitted not later than 4:30 PM (MDST) 09/10/04. Copies of the above-referenced clauses are available upon request, either by telephone or fax. By submission of an offer, the offeror acknowledges the requirement that a prospective awardee shall be registered in the CCR database prior to award, during performance, and through final payment of any contract, basic agreement, basic ordering agreement, or blanket purchasing agreement resulting from this solicitation. All responsible sources may submit an offer that will be considered by this Agency.
- Place of Performance
- Address: Rocky Mountain Laboratories, 903 South 4th Street, Hamilton, MT
- Zip Code: 59840
- Country: USA
- Zip Code: 59840
- Record
- SN00655274-W 20040828/040827093526 (fbodaily.com)
- Source
-
FedBizOpps.gov Link to This Notice
(may not be valid after Archive Date)
| FSG Index | This Issue's Index | Today's FBO Daily Index Page |