SOLICITATION NOTICE
B -- CONTINUE CONSTRUCTING A PLASMID DMA LIBRARY, SEQUENCING AND ANNOTATION SERVICES
- Notice Date
- 8/16/2005
- Notice Type
- Solicitation Notice
- NAICS
- 541710
— Research and Development in the Physical, Engineering, and Life Sciences
- Contracting Office
- Department of Agriculture, Agricultural Research Service, North Atlantic Area Office, 600 East Mermaid Lane, Wyndmoor, PA, 19038
- ZIP Code
- 19038
- Solicitation Number
- Reference-Number-5-1930-100-121
- Response Due
- 8/22/2005
- Archive Date
- 9/6/2005
- Description
- The USDA, Agricultural Research Service (ARS), intends to negotiate solely with Integrated Genomics in Chicago, IL to continue the sequencing of the Flavobacterium psychrophilum genome to close the remaining gaps in this genome sequence for the USDA, ARS, National Center for Cool and Cold Water Aquaculture (NCCCWA). The Contractor shall perform the following tasks to complete the Flavobacterium psychrophilum 2.5 megabase genome sequence project: 1) A Plasmid DNA Library has been previously constructed for the purpose of shotgun sequencing. An additional 30,000 sequence reads (400 bp Phred score 20) from this library must be obtained to result in a total genome coverage of >8 fold. 2) A Cosmid DNA Library must be constructed using 100ug of DNA provided from NCCCWA (isolate of interest and used to construct the Plasmid DNA library). 2000 paired end reads will be obtained from this library. 3) Assembly of new sequences and previous sequences to contigs using Phred/Phrap or comparable software. 4) Primer walking (2500 reactions) to close gaps between contigs. 5) The Contractor shall also combine new and previous data sets to perform final genome assembly and annotation by determination of open reading frames and metabolic reconstruction using proprietary ERGO bioinformatics. 6) Unused DNA and all clones from plasmid and cosmid libraries will be stored as frozen glycerol stocks will be returned to NCCCWA upon completion. 7) Sequence data will be in fasta format for the plain text sequence data and trace files in SCF format. All data must be formatted to match previously existing sequencing and annotation data. Gap #1 will be completed by amplifying across the gap and primer walking 2 kb of sequence. Gap #2 is spanned by fosmids. Identified fosmids will be grown, purified and sequenced. Gap #3 contains most of the repeat elements and extensive sequencing and assembly is required. Unique regions will be identified and closed by sequencing amplicons or isolating and sequencing overlapping fosmid clones. This gap requires assembly of a number of small repeated elements. The contractor guarantees closure of these gaps and any other misassemblies identified during closure of these gaps. The Contractor shall combine new and previous data sets to perform genome assembly and ERGO update of open reading frames and ORF calling and prepare information for the GenBank submission. The Contractor shall provide the bioinformatics expertise in ORF calling, ERGO analysis, and GenBank submission. The Government shall retain sole ownership of the data and clones. Work shall begin within 10 days after receipt of the order and completed by December 1, 2005. All deliverables shall be delivered FOB Destination to the USDA, ARS, National Center for Cool and Cold Water Aquaculture (NCCCWA) in Kearneysville, WV. The NAICS is 541710 with a size standard of 500 employees. This procurement is unrestricted. Companies with the demonstrated capability and financial capacity to provide and service such equipment must submit a written substantive statement outlining the Company's and systems' capabilities to the Contracting Officer within 5 days of publication of this notice. This is not a request for proposal. No solicitation is available.
- Place of Performance
- Address: USDA, ARS, National Center for Cool and Cold Water Aquaculture (NCCCWA), 11876 Leetown Road, Kearneysville, WV.
- Zip Code: 25430
- Country: United States
- Zip Code: 25430
- Record
- SN00871244-W 20050818/050816211639 (fbodaily.com)
- Source
-
FedBizOpps.gov Link to This Notice
(may not be valid after Archive Date)
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