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70 -- SEARCH SEQUENCE HARDWARE AND SOFTWARE Due 050595. POC Debra D. Vanderhoof, 703/883-8721. PRC Inc. in support of its prime contract with the Department of Commerce, the U.S. Patent and Trademark Office (USPTO), Office of Information Systems intends to award a sole source contract to MasPar Computer corporation (MasPar) for the provision of a nucleic and amino acid sequence similarity searching software system functioning on a massively parallel processor (MPP). The objective of this system is to augment the comprehensive and rapid sequence search capability to examine biotechnology patent applications containing sequence information, with advanced software features that permits USPTO examiners and research staff to construct highly specialized search queries corresponding to rapidly evolving advances in biotechnology inventions and associated patent claims, and quickly obtain search results to support timely examination efforts. During the patent examination process, it is imperative that USPTO complete a thorough test of the ``prior art'' in the public domain. For biotechnology patent applications containing nucleic and amino acid sequence claims, such a test involves application of the most sensitive sequence searching algorithm available. The MasPar MPP system includes the MPSRCH software from IntelliGenetics, Inc. This software includes a full implementation of the highly sensitive Smith-Waterman sequence searching algorithm that allows a search of DNA and protein databases for sequence similarity. In addition, the MPSRCH program incorporates these additional progra features used by USPTO: (1) supports an affine gap penalty for maximum sensitivity; (2) supports IUPAC codes and stop codons; (3) reports alignments and prediction values for each result; (4) reports percent matching residues for each result in the list of top scores and in the individual alignment output for each match; (5) supports BLOSUM, PAM and user-defined matrices; (6) employs a ranking function (corrected scoring function) for protein searches; (7) supports automated batch submission of multiple searches using predefined parameters by employing a graphical user interface (GUI) (Note: this interface is accessible from local workstations for sequence search submissions. The interface allows for complete automation of the sequence selection and searching process includig performing multiple database searches of both commercial and/or in-house (non-commercial) databases, performing range searching of sequences and performing oligomer searches); (8) employs reverse translation as method for comparing DNA queries with protein data banks and protein queries with DNA data banks; (9) ability of the search methods to handle the wide variety of biological redundancy present in DNA and protein sequences; (10) search procedures that handle both strands of the DNA sequences; (11) search procedures that allow amino acid substitutions according to PAM or BLOSUM matrices; (12) search procedures that either allow very long gaps (e.g. introns in genes) or disallow gaps (e.g. DNA probes, oligomers); (13) search procedures that allow condon substitutions in DNA coding regions; and (14) supports the creation of tabular output of search results, that allows for futher analytical processing. The MasPar hardware and software to be acquired by PRC is described as follows: MP-2216H, consisting of MasPar Massively Parallel MP-2216 System, 16,384 Processors and 1 GB RAM, PVME, DEC 3000 Model 300X AXP Desktop Workstation (32 MB), 1.05 GB Disk Storage, 600 OSF 1 AXP Operating System, MPPE, MPL Documentation; DA-6110A, Disk Array Unit with 10 disks, 1 controller, MasPar cabinet, 32 GB formatted capacity, 1 hot stand by, 1 parity disk; IO-0020B, IO Module with 128 MB IO RAM; MPSRCH for the MP2116 which includes software distributed on magnetic media (8MM Exabyte), for use on a single computer; MPSRCH User/Reference, and System Administrator Manuals; Software support for 12 months from the date of purchase; Data bank updates in IntelliGenetics Suite format for 12 months from date of purchase; MPSRCH data bank compression utility for EMBL, GenBank, DDBJ, SWISS-PROT, PIR (codata), FASTA, and IntelliGenetics Suite data bank formats. The hardware and software being acquired is an integrated system that is commercially available and available for delivery and production use within 30 days after contract award. PRC requires that the vendor of any sequence similarity searching software acquired must demonstrate that the products have successfully operated as part of a sequence data base searching service for public access. Further, PRC requires that any searching system acquired be fully compatible with existin SPARC hardware, and SunOS 4.x/Solaris 2.x operating system software at the USPTO. This is required to ensure that the existing hardware and software may continue to function as components of the network used to access the sequence searching software. See Note 22. (093)

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