SOLICITATION NOTICE
68 -- Genome Sequencing and Bioformatics Services
- Notice Date
- 8/14/2002
- Notice Type
- Solicitation Notice
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Institute of Allergy & Infectious Diseases/AMOB, 6700-B Rockledge Drive, Bethesda, MD, 20892-7605
- ZIP Code
- 20892-7605
- Solicitation Number
- RML-RFQ-2032
- Response Due
- 8/29/2002
- Point of Contact
- Julienne Keiser, Purchasing Agent, Phone 406-363-9370, Fax 406-363-9210, - Rebecca Guenthner, Chief Contracting Officer, Phone 301-402-2284, Fax 301-480-3695,
- E-Mail Address
-
Jkeiser@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 format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes being requested & written solicitation will not be issued. This procurement is being issued as a request for quotation. Submit offers on RML-RFQ #2032. Solicitation documents & incorporated provisions & clauses are those in effect through Federal Acquisition Circular 2001-08 dated 06/27/02. This acquisition will be processed under Simplified Acquisition Procedures (SAP) & is a Small Business Set-Aside. The North American Industry Classification System (NAICS) code for this procurement is 325414 & the small business size is 500. SCHEDULE: Laboratory of Human Bacterial Pathogenesis(LHBP), has published genome sequences of two serotypes of Streptococcus pyogenes. LHBP needs to determine chemical sequence of seven other S. pyogenes serotypes. This project includes 5 steps. Step1)Bioinformatics processing/analysis of 5 LHBP genomes. LHBP will deliver genomes to contractor for annotation & functional biochemical characterization using contractor bioinformatics infrastructure. Contractor shall perform annotation & analysis of genomes. Function to be assigned based on orthologous clustering, gene context/pathway reconstruction. Contractor will provide hardware/software/processed data to LHBP. Seven M serotypes, Streptococcus pyogenes genomes, need to be sequenced in three steps: 1) library construction, 2) 10X shotgun sequencing, & 3) genome finishing, leading to 5-10 contigs at average Q40 or higher per MB. Step2) library construction. Ea. Genome to be approx. 2.0MB in size. LHBP will send contractor purified total genomic DNA. Contractor will use DNA to construct two libraries, at ninety percent or greater cloning success, per genome/M-type. One library will be constructed using plasmid vector pGEM-3Z, where DNA is to be fragmented to average size of 2 kb and cloned. Second library using Loris 6 cosmid vector where fragments are generated by partial digestion, larger than 10kb, and cloned. Step3) 10X shotgun sequencing/preliminary annotation/comparison. Both libraries, transformed colonies, will be grown in petri trays & picked into 96 well plates by a robot at 3,000 colonies per hour. Ea. colony/clone must be named reflecting the organism, type of the library, cloning attempt, ID of 96-well plate & it's relative position in the plate. DNA will be purified from clones via mini-preps using robots. 96 well plates with purified plasmid DNAs must be stored in dedicated, specific freezers at -20 Celsius. Sequencing reactions will be performed in 384-well plates. IDs of 96-well plates must transfer to 384-well format. Sequencing reactions performed using ET MegaBACE Dye Terminator Kit. Sequencing reactions may be loaded onto MegaBACE 1000 DNA sequencers or ABI 3700 DNA sequencers. Samples sequenced from both ends, forward & reverse, using vector-specific primers for both plasmid libraries. Passing sequence reactions will be at 500 bases of Q19-20 level or higher. A minimum of approx. 40,000 sequencing reactions at 500 bases length or higher, & Q19-20 quality or higher, for ea. genome. Approx. 10,000 reads or higher must be performed ea. day during shotgun phase for ea. genome. 5-10% of total number of reads from cosmid library, while the rest will come from PGEM-3Z library. 10X assembly should produce between 100 & 250 contigs per genome. Contractor will compute, based on assembled sequences & summing sizes of contigs, better estimate of genome sizes. Contractor will do extra runs to bring the average coverage to 10X. Total number of runs must not exceed 40,000 per genome without written approval by the RML Project Officer. Primary assembly of individual sequences performed using Phred/Cross_match/Phrap package. Following 10X assembly, data will be annotated. Genomes will be compared against all similar species publicly available or present at RML. A list of unique & conserved ORFs for ea. genome will be produced & transferred to LHBP. 10X sequencing reads & assemblies will be delivered & must be compatible with our Finch server(www.geospiza.com). Contractor will perform QC and forensic PCR tests to ensure no contamination between genomes during Step 2-3. Step4) Genome Finishing, annotation & comparison. Several rounds of primer-walking/manipulations with layout to be performed using Consed/AutoFinish editing software. Additional custom sequencing/PCR will be used to verify layout of reads, order (scaffold) contigs, raise quality levels for problem regions & join contigs. Full, automated analysis involving ORF calling, gene annotation & functional reconstruction of genomes using an advanced bioinformatics system to be performed. Three rounds (1-3) of functional assignments for all genes/every genome should be performed, two before completion of metabolic reconstruction, one after. Round 1 to be performed by algorithms that automatically predict function for as many genes as possible in genome. Round 2 to involve a detailed manual analysis by human experts. Manual inspection must involve use of more sensitive sequence similarity search tools as motif/pattern databases Pfam, Prosite, Prodom, & COGs. Contractor algorithms that explore predictive power of chromosomal clustering must be employed to predict putative function. When genes are assigned with functions, they should be placed in corresponding cellular pathways, with high detail & depth. Contractor should have a cellular pathway database with more than 5,000 cellular pathways. Expert manual curator must decide which of entire set of available pathways should be present for organism under study, & must provide a report for ea. genome. All possible connections across pathways must be delineated. An "in silico" reconstruction of organism must be produced. Functions expected, but are not present, will need to be identified. ORFs or pathways that are present/not present in sequenced strains, must be identified by genome comparison analysis, using LHBP genomes/public genomes. Round 3 will be manual & involve querying the function predicted present, against target. Contractor performs visit three days on site, for installation/training of database server. Government will supply LHBP sequenced genomes, a set of emm-specific/generic primer pairs & generic 16s primer pairs for Forensic PCR QC, text files of these sequences, purified, specific, genomic DNA for seven strains, suitable for library construction. DNAs will be supplied in 70% EToH & sent in time-separated manner to avoid genome contamination. Contractor to provide status reports. DELIVERABLES: Contractor will produce/provide following deliverables for Step 1. Contractor will identify Open Reading Frames (ORFs), perform comparative analysis, and construct biochemical pathways for ea. five genomes supplied by LHBP. Gene annotation for ea. genome converted to flat file format/delivered to RML on CD& installed at RML on contractor-supplied server. In addition to five mentioned RML genomes, contractor database will contain annotation/functional information for at least 80 publicly available prokaryotic genomes. Installation of contractor server must include 32 hours instruction. Contractor-supplied system must have following hardware configurations: Series 220, PIII, 1.26 GHz/133MHz, 512KB open HS bay, tower (1x). IBM dual processor server with 1GB RAM, floppy, CD-ROM drive, keyboard, 3-button mouse, UPS. IBM 18GB 10K-4 Ultra160 SCSI HotSwap SL HDD (1x) & IBM 36.4 GB 10K Ultra160 SCSI Hot-Swap SL HDD (1x). Software to include RedHat Linux 7.2. & contractor database/software system. Duration of Step 1: Not to exceed 6 weeks from the receipt of genome sequences from RML. Contractor to produce/provide following deliverables for Step 2.1) One plasmid library per genome with >90% clones containing insertion fragments larger than 2kb. (7 total). 2) One cosmid library per genome containing fragments 10 kb or larger. (7 total). Duration of Step 2: Not to exceed 3 weeks after receiving genomic DNA for ea. genome. Contractor to produce/provide following deliverables for Step 3.1) Approximately 40,000 sequencing reactions per genome, or number of reads needed to reach the 10X sequencing coverage level. Trace data for at least 40,000 reactions will be in SCF format & posted on contractor's secure server available for FTP download. Sequence data must be compatible with our Finch server. Sequence data must be convertable to FASTA format. 2) Purified plasmid DNA of clones must be stored in dedicated freezers at contractor's site. All plasmid/cosmid DNA to be ready for shipment to RML in 96-well format, on dry ice, within 24 hrs of request for those DNAs. Following 10X shotgun sequencing of genome, assembly will be converted to flat file format (FASTA) & delivered to RML on CD within 5-10 days of assembly completion. 3) Preliminary annotation of assembly to be converted to flat file format/delivered to RML on CD mentioned above. In this annotation, those ORFs/Intergenic regions that appear to be unique or conserved for that genome in comparison with known Streptococcus genomes at that time will be highlighted. Duration of step 3: Not to exceed 4 weeks from completion of Step1 for ea. genome. Contractor will produce/provide following deliverables for Step 4.1) Trace data for all primer-walking/finishing reactions in SCF format, to be posted on contractor's secure server available for FTP download. 2) Following 10X shotgun/finishing of genome, assembly & gene annotation to be converted to flat file format & delivered to RML on CD. 3) Same set of gene annotation data to be installed on contractor delivered server (step 1) via a swappable hard drive delivered to RML. Cellular & metabolic pathway reconstruction for ea. genome to be available on this server.4) All data generated within scope of project will be completely deleted from Contractor's equipment upon completion of contract, unless otherwise specified by RML Program Officer. 5) List of all unique & conserved ORFs/intergenic sequences for ea. genome to be provided in flat file format. Duration of step 4: not to exceed 3 months from completion of Step 2. Contractor will produce/provide following deliverables for Step 5. 1) Final set of gene annotation for all 12 sequenced & analyzed LHBP genomes, including any new finishing/sequencing data generated by RML prior to week 44, to be installed on contractor delivered server (step 1) at the RML site. Installation to include an additional 8 hours of tutorial instruction on-site. Duration of step 5: Not to exceed 2 weeks from completion of Step 4 for last three genomes. FOB Point shall be Destination, Hamilton, MT. Delivery as annotated above. The following FAR provisions & clauses apply to this acquisition: FAR52.212-1 Instructions to Offerors-Commercial; FAR52.212-2 Evaluation-Commercial Items; FAR52.212-4 ContractTerms&Conditions-Commercial Items;FAR52.212-5Contract terms & Conditions Required to Implement Statues or Executive Orders-Commercial Items; FAR52.246-2 Inspection of Supplies-Fixed Price. Offerors must include along with their offer a completed copy of the provisions at FAR52.212-3 Offerors Representations & Certifications-Commercial Items. Warranty information to include period & coverage, shall be stated. Award will be based on capability of item offered to meet above stated salient characteristics, delivery, price & past performance. Offers may be mailed or faxed to POC indicated above (Fax 406-363-9288). Offers must be submitted not later than 4:30 PM(MDST), August 29, 2002. 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 Labs, 903 South 4th Street, Hamilton, MT
- Zip Code: 59840
- Zip Code: 59840
- Record
- SN00140377-W 20020816/020814213257 (fbodaily.com)
- Source
-
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