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2430    PatentIn Information; Utilities Programs; Training [R-08.2012]

In those areas of biotechnology in which nucleotide and/or amino acid sequence information is significant, many patent applicants are accustomed to, or familiar with, the submission of such sequence information, in electronic form, to various sequence databases, such as GenBank, which is produced by the National Institutes of Health. In order to facilitate such submissions, or merely for the purpose of researching and developing sequence information, many eventual patent applicants also generate or encode sequence information in computer readable form. In order to further facilitate compliance with the sequence rules, the Office previously made available to the public an input program based on the AuthorIn program produced by GenBank. This input program, called PatentIn version 1.3, was specifically tailored to the requirements of the sequence rules which were in effect between October 1, 1990 and July 1, 1998.

The current sequence rules, which are embodied in 37 CFR 1.821-1.825 and World Intellectual Property Organization (WIPO) Standard ST.25, became effective July 1, 1998. The rules simplify the Sequence Listing requirements, and harmonize the format among all Trilateral Offices and many other patent offices around the world. The Office deployed PatentIn versions 2.0 and 2.1, in 1998 and 1999, respectively, incorporating changes in the required format for the Sequence Listing to ensure compliance with the sequence rules that became effective July 1, 1998. These versions operated under Microsoft Windows 3.1x, 95, 98 and NT. By using PatentIn version 2.0 or 2.1, customers were able to generate a Sequence Listing once and use that same listing to file at multiple patent offices worldwide. Applications filed in the U.S. after July 1, 1998 containing Sequence Listings prepared using PatentIn version 1.3 will not be in compliance with the U.S. sequence rules. Applications filed in the member countries of WIPO after July 1, 1998 containing Sequence Listings prepared using PatentIn version 1.3 will not be in compliance with ST.25.

In June 2000 another update of PatentIn was deployed, version 3.0. This version differs from earlier versions in that the capabilities have been extended. PatentIn 3.0 has several advantages over PatentIn 2.1. PatentIn 3.0 processes large sequences (over one million bases) and applications with a large number of sequences (over 100,000); it imports multiple sequences from a single file as well as multiple sequences from multiple files. Features defined for nucleic acid sequences are carried over to the supplemental amino acid sequences generated by the CDS feature. PatentIn 3.0 is more user-friendly than PatentIn 2.1 and looks and feels more like other Windows-based programs. Unlike PatentIn 2.1, projects are portable from one computer to another provided PatentIn 3.0 is installed. From a programming viewpoint, the advantages include that the overall lines of code have been reduced to 25 percent of that required by PatentIn 2.1, maintenance of the code is easier since it is written in Visual C++ and it is easier to modify the code.

In March of 2001 PatentIn 3.1 was released. This newest version builds on the success of PatentIn 3.0 and expands its capabilities. One difference is that the capability to import a single sequence from a single file without a header has been added. The definition of variable characters has been enhanced in PatentIn 3.1. If the nucleotide sequence has the variable “n” and the CDS feature is selected, PatentIn 3.1 will calculate the position of the necessary Xaa in the supplemental protein sequence and provide the definition automatically based on the codon in which the “n” appears.

PatentIn version 3.1, and the companion User’s Manual, are available on the Office World Wide Web site ( for free downloading. Copies of both the program and the user manual may also be purchased from the Office on 3 1/2-inch floppy diskette or compact disc. PatentIn 3.1 operates in a Windows 95/98/NT/2000 environment and has similar space, memory and system requirements as those for PatentIn version 3.0. A minimum of 64 MB of memory is recommended for smaller projects. Otherwise 128 MB is recommended. Even more additional memory may be required for larger sequence listings. The disk space required to install PatentIn 3.0 is 1.6 MB. Additional disk space is required to store project files and sequence listing files.

See MPEP § 1730 for additional information regarding ordering and using PatentIn.

While use of the PatentIn program is not required for compliance with the sequence rules, its use is highly recommended as Office experience has shown that submissions developed with PatentIn are far less likely to include errors than those developed without the program. The many automatic features of the PatentIn program also greatly ease the generation of Sequence Listings when compared to generating them by hand in a word processing environment. This is especially true for Sequence Listings that include many sequences and/or sequences having great lengths.

The Office provides hands-on training in the use of the PatentIn and associated utilities programs. The classes are held in Washington D.C. as demand warrants. In addition, on site training may be arranged at locations outside Washington, D.C. To express interest in such classes, please contact the Search and Information Resources Administration.



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Last Modified: 03/27/2014 10:10:34