SOLICITATION NOTICE
68 -- Genome Sequencing
- Notice Date
- 9/7/2004
- 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-4043
- Response Due
- 9/22/2004
- Archive Date
- 10/7/2004
- Point of Contact
- Jenny Lovitt, Purchasing Agent, Phone 406-363-9489, Fax 406-363-9288, - John Foley, Contracting Officer, Phone 301-402-2284, Fax 301-480-0689,
- E-Mail Address
-
jlovitt@niaid.nih.gov, jfoley@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 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-4043. 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 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 one genome, which will include sequencing, assembly and professionally annotating a genome to total completion. The Genome sequencing shall involve three phases as follows: Phase I: 1) Two genomic libraries shall be constructed by random, mechanical shearing. One library shall contain inserts of 2-3kb, the other up to 40kb. Libraries shall be non-amplified, Quality Control tested for ligation, size distribution of fragments, clone integrity and quality of paired-end sequencing. 2) Clones shall be picked for template purification and freezer storage by robotic colony picking robots. 3) Templates shall be isolated by alkaline lysis and sequenced by PCR using the di-deoxy method of Sanger and vector?specific primers. 4) Shotgun sequencing shall be performed to 7X, based on predicted size of the genome from first 2000 reads. No other project or sequencing effort shall interfere or intermingle with the continuous shotgun genome effort described for this genome. 5) Two to three rounds of auto finishing shall be performed. Genome assemblies shall rely on proven contractor-based assemblers or publicly available assembler software. Completion of Phase I shall be no later than 3 months after receipt of government furnished materials. Phase II: Closure 20 contigs/MB genome shall be performed including 1) primer walking to ungapped assembly; 2) manual editing of read and contig sequences and manipulation of the layout; and 3) ORF calling and automated annotation. Completion of Phase II shall be no later than 2 months after completion of Phase I. Phase III: Ungapped Assembly and annotation of the completed genome shall be performed including: 1) Multiple rounds of primer walking to reach ungapped assembly; 2) Manual editing of read and contig sequences, and manipulation of the layout to reach ungapped assembly; 3) a first round automated analysis for ORF calling and functional analysis using BLAST, motif searches, gene context, Signal PtRNAScan or other proven and appropriate software shall be performed for the finished ungapped genome; 4) a second round of manual analysis for annotation purposes focusing on related annotated genomes for comparative purposes; 5)analysis of gene conservation; and 6) delivery of conservation/unique data analysis in flat file format on CD. Completion of Phase III shall be no later than 4 months after completion of Phase II. Deliverables shall be: Trace data for all primer-walking/finishing reactions, in SCF format, shall be available for ftp download. Contigs in flat file format shall be delivered on CD. Gene annotation and pathway information shall be delivered by flat file (EMBL format) on CD. A list of unique and conserved ORFs and DNAs for the genome, as compared to all existing related genomes, shall be provided in flat file format on CD, with a final list for the new genome compared to all other closely related, publicly available genomes following the completion of Phase III. A preliminary draft of the single contig/chromosome assembled where the total genome is at Q40 or higher with no more than one error per 10,000 bases shall be delivered in flat file format on CD. Data upload to the RML ERGO server shall be performed. Internet connectivity to Contractor?s graphics-based genome data analysis and data interpretation interface shall be provided. The Project Director shall provide weekly status/progress reports to the RML Project Officer on a weekly basis by e-mail. 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; and 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 - 406-363-9288). Offers must be submitted not later than 4:30 PM (MDST) 09/22/04. 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 form this solicitation. 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 South 4th Street, Hamilton, MT
- Zip Code: 59840
- Country: USA
- Zip Code: 59840
- Record
- SN00666137-W 20040909/040907211722 (fbodaily.com)
- Source
-
FedBizOpps.gov Link to This Notice
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