SNOTE | B | FULL GENOME SEQUENCING ANALYSIS OF METARHIZIUM ANISOPLIAE, ARSEF 2575

FBO DAILY ISSUE OF AUGUST 13, 2008 FBO #2452
SPECIAL NOTICE

B -- FULL GENOME SEQUENCING ANALYSIS OF METARHIZIUM ANISOPLIAE, ARSEF 2575

Notice Date: 8/11/2008
Notice Type: Special Notice
NAICS: 541711 — Research and Development in Biotechnology
Contracting Office: Department of Agriculture, Agricultural Research Service, North Atlantic Area Office, 600 East Mermaid Lane, Wyndmoor, Pennsylvania, 19038
ZIP Code: 19038
Solicitation Number: 801-1907-101-545
Response Due: 8/18/2008 5:00:00 PM
Archive Date: 9/30/2008
Point of Contact: Lisa M. Botella,, Phone: 215-233-6551
E-Mail Address: lisa.botella@ars.usda.gov
Small Business Set-Aside: N/A
Description: The USDA, Agricultural Research Service (ARS), intends to negotiate solely with the University of Oklahoma in Norman, Oklahoma to provide a full genome sequencing analysis of Metarhizium ansiopliae, ARSEF 2575 in order to expand our ability to manipulate the fungus for more effective biological control. It is clear from this recent progress that while M. anisopliae ESTs have revealed important surprises, the design of studies will be vastly improved when informed by the full genome sequence of this unique experimental system. In particular, it will facilitate functional genomic research to enhance stress tolerance, virulence, efficacy and wider use of fungi in biocontrol. For these reasons, the USDA, ARS, Biological Integrated Pest Management Research Unit requires a Contractor to provide 454 GS-FLX massively parallel pyrosequencing on genomic DNA from Metarhizium anisopliae ARSEF 2575 for full genome sequencing. Sequencing will generate 16X coverage to allow for full genome assembly. The contractor will provide an average minimum length read of 250 phred20 bases per read and a minimum of 70 million bases per full plate run, with a total of 6 full plate runs. Requirements include the delivery of all raw data in Fasta format as well as the data clustered via Newbler assembler in FastA format with blast homology hits for both raw sequence and assembled data. Delivery is required 90 days after receipt purchase order award and vendor receives required DNA from the filamentous fungus Metarhizium anisopliae supplied by USDA, Biological Integrated Pest Management Research Unit.  A)  The Government shall provide: 1.  Prepare 20 ug of genomic DNA with an average length of 20,000 bp.  2.  DNA samples in acqueous solution at 0.5 m g/ m l concentration.  3.  Shipment of DNA samples will be packed on dry ice via Federal Express overnight delivery within 30 days after contact award. B.  The Contractor shall provide: 1. 454 massively parallel pyrosequencing for 16X coverage of full genome analysis of Metarhizium anisopliae 2575. 2. DNA sample to be prepared for 454 sequencing analysis. 3. Guarantee that sequence read with an average minimum read length of 250 phred20 bases per read and a total of at least 70 million bases per full plate run of 454 GS-FLX sequence. 4. Total raw sequence data in Fasta format along with the quality scores, and the data clustered with the Newbler assembler in FastA format with quality scores, as well as the top 5 blast homology hits for the raw sequences and/or assembled data in FastA format within 90 days after receipt of the DNA samples. 5. Conduct 6 full plate sequencing runs for a total of 16x coverage of the genome. Sole Source Justification: The University of Oklahoma has: 1) A proven track record of sequencing fungal genomes; guaranteed minimum of 70 million bases per full plate run; Guaranteed minimum average read length of 250 bases/sequence; All raw data provide to ARS; Newbler assembled data provided; Blast analysis conduction on each sequence; maximum of six (6) full plate runs for 16x coverage and sequencing completed within (90) days of receipt of DNA sample; if problems arise, the Contractor will trouble shoot issues with the USDA in order to resolve issues and provide the sequencing data as specified. The NAICS is 541711 with a size standard of 500 employees. This procurement is unrestricted. This is not a request for proposal. No solicitation is available. Companies with the demonstrated capability and financial capacity to provide this service must submit a written substantive statement outlining the Company’s and service capabilities, including the consumables (and price lists). This announcement and any other documents related to this procurement will be available electronically at the Internet site http://www.fbo.gov. The Contractor is responsible for monitoring the FBO website for information relating to this requirement. Offerors will be responsible for downloading their own copy of these documents. Contractors are required to acknowledge receipt of all Amendments (if any). If no affirmative responses are received with 5 calendar days of publication of this notice to determine whether a qualified source is more advantageous to the Government, an order will be placed with University of Oklahoma under the authority of FAR 6.302.
Web Link: FedBizOpps Complete View
(https://www.fbo.gov/?s=opportunity&mode=form&id=71fe5342441aac3109dd146c2d7b2142&tab=core&_cview=1)
Place of Performance: Address: USDA, ARS, NAA, Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, New York, 14853-2703, United States; Zip Code: 14853-2703
Record: SN01636332-W 20080813/080811223014-71fe5342441aac3109dd146c2d7b2142 (fbodaily.com)
Source: FedBizOpps Link to This Notice
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B -- FULL GENOME SEQUENCING ANALYSIS OF METARHIZIUM ANISOPLIAE, ARSEF 2575