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FBO DAILY ISSUE OF APRIL 17, 2003 FBO #0503
SOLICITATION NOTICE

68 -- Genome sequencing and closure

Notice Date
4/15/2003
 
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
Reference-Number-RML-RFQ-3023
 
Archive Date
5/15/2003
 
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
 
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-3023. The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2001-13 dated 04/17/03. 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 the DNA of Chlamydia trachomatis, which will include sequencing, assembly and professionally annotating a Chlamydia genome to total completion. Genome sequencing involves two phases. Phase I:1)library, 2)10X shotgun sequencing, 3)assembly, 4)annotation and ERGO incorporation. Phase II:1)genome finishing and assembly, 2)final annotation and final ERGO incorporation. Independently, and not as an agent for the government, the contractor shall provide to LICP, services from qualified and experienced personnel. Labor categories shall include: Project Manager, Bioinformatics Scientist, Software engineer, Technical Personnel, and others as may be suggested by the vendor and approved by the Project Officer. This is an 8-12 month, one time work effort, where the final product will be the complete sequence of a Chlamydia genome with Q40 or higher quality per base. Files must be compatible, transferable to and readable by the bioinformatics software and RML computing systems and infrastructure which involves a Finch server (www.geospiza.com), ERGO server and other RML systems, which are PC, MAC and Unix/Linux-based. PHASE I: Library, 10X, gap closure, assembly, annotation/comparison, ERGO incorporation with the following deliverables: 1) One plasmid library where >90% clones contain inserts at, or larger than 2kb. 2) Sequencing reaction trace data for all reads shall be in SCF format and shall be posted on the Contractor?s secure server available for FTP download. The trace data shall be readable by our Finch server and standard sequence editing software. 3)Purified plasmid DNA of sequenced clones shall be available for shipment to RML in 96-well plate format on dry ice within 24hrs of notice of request for those DNAs. 4) Flat file of the assembly at 5 to 20 contigs per 1 Mb. Delivery of the preliminary annotation and unique/conserved comparison results in flat file format on CD, along with RML-ERGO data incorporation by secure tunnel. STEP 1) Library construction. The Chlamydia genome is estimated to be approximately 1.01MB in size, with zero to two extrachromosomal plasmid-like elements. LICP will send to the contractor purified genomic DNA for library construction. The contractor shall use this DNA to construct a library using the plasmid vector pGEM-3Z. DNA will be fragmented using a sterile, computer controlled shearing device to achieve an average DNA fragment size of 2 KB. Ninety percent or greater cloning success of 2kb fragment representation in the clones shall be achieved. Progressive assemblies of the incoming data shall begin after the first 1,000 clones from the library have been sequenced to test quality and randomness of the library. STEP 2) 10X shotgun sequencing. The colony picking robot shall be capable of picking at least 3,000 colonies per hour. Each clone shall receive an individual name reflecting the organism, library, the cloning attempt, the plate ID and position. Cultures shall be processed for DNA mini-preps using robots for plasmid extraction and purification steps. 96 well plates with purified plasmid DNAs shall be stored in dedicated, specific freezers. IDs of the 96- well plates shall transfer to the 384-well format for tracking. Sequencing reactions shall be performed using the ET MegaBACE Dye Terminator Kit (Applied Biosystems). Test reactions shall be optimized prior to loading the bulk of the 10X reactions for sequencing. Passing sequencing reactions shall average at least 400 bases or longer of average Q20 or higher quality per read. A minimum of approximately 22,000 sequencing reactions at 400 bases or longer at Q20 average quality or higher per read, shall be performed. 5,000 reads or more shall be performed each day. The assembly shall produce between 100 and 250 contigs or gaps per genome. The contractor shall compute a size estimate of the genome. LICP recognizes that genome size is an unknown and may vary from the 1.01MB estimate. If the total number of runs brings the coverage to slightly greater than 10X, this extra coverage will be useful to LICP. The total number of runs per genome shall not exceed 22,000 without written approval by the RML LICP Project Officer. STEP 3) Primary assembly. Assembly shall be performed using Phred/Cross_match/Phrap. The contractor shall have additional in-house tools to help the preparation of the data for assemblies. The assembly dynamics shall be monitored and compared with models. The integrity of the assemblies shall be checked using either in-house or commercial tools. The assembled data shall be annotated and compared against all known related species/strains publicly available. A list of unique and conserved ORFs for each genome shall be produced and delivered to RML, LICP. 10X sequencing reads and assemblies shall be delivered and must be compatible with our Finch server (www.geospiza.com). STEP 4) Genome Finishing, annotation and comparison, RML-ERGO incorporation. Following several rounds of primer-walking and manual editing of read and contig sequences, additional sequencing or PCR shall also be used to verify and correct the assembly. Full, automated analysis involving ORF calling, gene annotation and functional reconstruction of the genome shall be performed. Three rounds of functional assignments for all genes shall be performed. Manual analysis by human experts shall be performed. Chromosomal clustering shall be performed in the absence of sequence similarity. The contractor cellular database shall contain 5,000 or more cellular pathways. The contractor shall determine which functions are expected to be present in this organism, yet have escaped identification. The contractor shall identify those ORFs or pathways that are present or not present by comparing known genomes available for Chlamydia. The data shall be transferred into the RML-ERGO server by secure tunnel and be compatible and viewable in all formats and annotations currently in the RML-ERGO server at this time. Duration of PHASE I: Not to exceed 14 weeks. The Project Director shall provide Status/progress reports to the RML Project Officer on a weekly basis by e-mail. PHASE 2: Genome finishing, final assembly, final annotation, RML-ERGO data incorporation, with the following deliverables: 1) All trace data for all primer-walking/finishing reactions performed during this phase. These reactions shall be in SCF format and shall be posted on the contractor?s secure FTP site for download. The trace data will be readable by any standard sequence editing software. 2) Single contig per genetic element at Q40 or higher quality per base following final assembly. The assembled sequence shall be converted to flat file format and delivered to RML on a CD. 3) Gene annotation/comparison data shall be converted to flat file format and delivered to RML on the CD described above. 4) A list of all-unique and conserved ORFs and intergenic sequences for the sequenced genome as compared to all publicly available Chlalmydia genomes shall be provided in flat file format on the CD described above. RML-ERGO data incorporation by secure tunnel of the genome data shall also be performed. STEP 1) Genome finishing/polishing, Gap Closure, assembly. The contractor shall perform gap closing, genome polishing and genome finishing. Manual analysis and verification of each base pair in the consensus shall be performed. Contractor algorithms shall be used for verification of the assembly. Additional sequencing from the chromosome and PCR products shall be performed. The final result shall be one high quality contig corresponding to the chromosome of the Chlamydia genome, and 1 or 2 contigs corresponding to extra chromosomal elements, if present. Quality of the individual bases shall be at Q40 or higher throughout the genome sequence. STEP 2) Final annotation, RML-ERGO incorporation. Three rounds of ORF functional assignments shall be performed involving predicting the gene function based on ortholog and protein family clusters, manual analysis by human bioinformatisists and analysis of functions expected to be present, yet have escaped identification. The contractor shall have 5,000 cellular pathways for comparison. This database will allow for construction of the ?in silico? reconstruction of the organism. Arguments shall be made regarding why a particular function may be absent in a given pathway. A significant increase in the function prediction coverage (on average 10-20% for the genome), shall be produced as compared to publicly available annotations. The data shall be transferred into the RML-ERGO server by secure tunnel. The data shall be compatible with the 80+ genome data currently in the RML-ERGO server at this time. Duration of the PHASE II: Not to exceed 4 months from the moment of completion of Phase 1. The Project Director shall provide 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. 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) 04/30/03. 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
 
Record
SN00303996-W 20030417/030415213339 (fbodaily.com)
 
Source
FedBizOpps.gov Link to This Notice
(may not be valid after Archive Date)

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