PatentIn Version 3.5: Windows XP/Windows Vista Release Notes and Installation Instructions

PatentIn version 3.5 is enhanced with the latest Microsoft .NET technology to provide better software performance, accessibility, and reliability.  Now a PatentIn-generated ST.25 Sequence listing file can be imported to the PatentIn system for further sequence data modification and can be regenerated to produce a new sequence listing.  It can also process a sequence as large as 12 MB and generate a sequence listing up to, but not limited to, 12 MB.   In addition to the posting of PatentIn 3.5 the USPTO has elected to remove the link to PatentIn 3.3.

PatentIn version 3.4 is enhanced with the Microsoft .NET technology to provide better software performance, accessibility and reliability. Sequence listing generation is also strengthened with more validity checks.

PatentIn version 3.3 enhances PatentIn version 3.2 and it is friendlier to use.

PatentIn 3.2 is an enhanced version of PatentIn 3.1 and contains some additional features designed to ease the authoring of sequence listings.

PatentIn 3.1 is a computer program designed to expedite the preparation of patent applications containing nucleic acid and amino acid sequences. PatentIn 3.1 generates sequence listings that comply with all format requirements specified in the World Intellectual Property Organization (WIPO) Standard ST.25 and the related U.S. final rule, "Requirements for Patent Applications Containing Nucleotide Sequence and/or Amino Acid Disclosures," 37 CFR §§1.821 - 1.825 effective July 1, 1998. It has been tested on Windows 95, Windows 98, Windows NT and Windows 2000. It is expected to run on Windows Me as well but has not been tested on that operating system.

PatentIn 3.1 built upon the advances made by PatentIn 3.0 to create a more useful sequence listing authoring tool. PatentIn 3.1 was intended to replace PatentIn 3.0. Since PatentIn 3.1 could import PatentIn 2.1 files it was also intended to replace PatentIn 2.1. Questions on PatentIn 2.1 may be directed to the help personnel for PatentIn 3.1.

Training in how to use this software is offered at the USPTO from time to time. It is also possible for training to be provided off-site as well, if arranged in advance and approved by the USPTO. Please contact Mr. Christopher Low at (571) 272-0951 for further information.

Key enhancements over PatentIn 3.4 included in PatentIn 3.5:

• PatentIn version 3.5 is enhanced with the latest Microsoft .NET technology to provide better software performance, accessibility and reliability.  It sets a foundation for the next wave of computer technology.
• A PatentIn generated ST.25 Sequence listing file can now be imported to the PatentIn system for further sequence data modification and can be re-generated to produce a new sequence listing based on the enhanced sequence data.  (Note: It is necessary for PatentIn users to verify if the imported sequence information is interpreted and stored in the PatentIn system as anticipated after the import process since the data may or may not be converted to be 100% compliant with the imported ST.25 sequence listing.)
• PatentIn 3.5 is capable of processing a single sequence as large as 12MB and generating an ST.25 sequence listing up to but not limited to 12MB.
• In addition to Windows XP, PatentIn 3.5 can also run on Windows Vista.
• PatentIn 3.5 is powered by the latest upgraded data compression software to enhance the “Copy to Disk” operation.
• PatentIn 3.5 uses the latest Windows Installer technology to provide easier, safer and more reliable installation and uninstallation of PatentIn 3.5.
• PatentIn 3.5 has been tested on Windows XP, Windows Vista Ultimate, Windows Vista Home Basic and Windows Vista Home Premium. It may or may not run on any earlier versions of Windows, which are no longer supported by Microsoft.

Key enhancements over PatentIn 3.3 included in PatentIn 3.4:

• PatentIn 3.4 is migrated to Microsoft .NET technology. It provides better software performance, accessibility and reliability. It sets a foundation for the next wave of computer technology.
• Sequence validation is more stringent with new rules. New warning messages will be generated by PatentIn 3.4 for any primary sequences containing less than 10 nucleotides or 4 amino acids.
• PatentIn 3.4 is enhanced to be Section 508 compliant. Access keys (shortcut keys) have been programmed to activate all PatentIn screen buttons and checkboxes in addition to PatentIn menus. The tab key can also be used to navigate through all PatentIn screens. This enhancement not only gains better accessibility to PatentIn software, but also increases users’ speed and efficiency while using PatentIn. The help on how to use PatentIn access keys can be found from PatentIn on-line Help menu. Please note that some access keys for PatenIn menus have been changed from PatentIn 3.3.
• PatentIn 3.4 is powered by the upgraded data compression software to enhance the “Copy to Disk” operation.
• PatentIn 3.4 uses Windows Installer technology to provide easier, safer and more reliable installation and uninstallation of PatentIn 3.4. It also does self-repairing if it detects that files needed to run PatentIn 3.4 are missing or corrupted.
• All PatentIn 3.4 generated output file names have been changed to adapt commonly used file naming convention. The new formats for these file names are indicated as follows:

sequence listing file: <PatentIn Project Name>_ST25.txt
error log file: <PatentIn Project Name>_ErrorLog.txt
work progress file: <PatentIn Project Name>_WorkFile.txt

• Under this release PatentIn 3.4 no longer converts PatentIn 2.1 data format to PatentIn 3.X data format. Therefore, there is no need to install Microsoft Access 97, which is no longer supported by Microsoft, to run all features provided by PatentIn 3.4. If a user wishes to import PatentIn 2.1 files, the previous version (PatentIn 3.3) can still be downloaded via the link provided at the bottom of this page. Please note that this support is only available for a limited time.
• PatentIn 3.4 was tested on Windows XP. It may or may not run on any earlier versions of Windows, which are no longer supported by Microsoft.

Key enhancements over PatentIn 3.2 included in PatentIn 3.3:

• Users do not have to remove the sequence bases from the sequence editor and then delete the related feature and publication information in order to skip a sequence during the sequence listing generation. A checkbox has been added to the sequence window to indicate if a sequence should be skipped. The sequence will be skipped if the box is checked and all data related to the skipped sequence can remain in the PatentIn 3.3 project during the sequence listing generation.
• PatentIn 3.3 allows sequence type conversion between non-protein type sequences by clicking on the new AlterSeqType button on the sequence window.
• Direct access from the main window to the database window instead of the journal window is provided in PatentIn 3.3. The system also provides direct access from any publication window to any other publication windows.
• More date validations are added to PatentIn 3.3. For example: all dates entered into the sequence listing must be earlier than the current date; the Current Filing Date must be more recent than the Prior Application Filing Date; and, the Publication Date must be more recent than the Filing Date.

Note: Due to the serialization change to the stored data in PatentIn 3.3, PatentIn data created from PatentIn 3.3 cannot be read by or brought to PatentIn 3.x version prior to version 3.3. However, PatentIn 3.3 can read all data created from any PatentIn 3.x.

Key enhancements over PatentIn 3.2 version 3.2.2 included in PatentIn 3.2 version 3.2.3:

• PatentIn 3.2 version 3.2.3 enables users to run PatentIn on Windows NT 4.0 systems with a version of system shell32.dll prior to 4.71. It solved the missing entry point problem for this special case.
• PatentIn 3.2 version 3.2.3 generates “Synthetic Construct” for the numeric identifier <223> in the protein sequence generated from any coding region in a nucleotide sequence where Artificial or Unknown is used as the organism.
• PatentIn 3.2 version 3.2.3 removes numeric identifiers <220> and <223> entries if an organism name is changed from "Artificial" or "Unknown" to something else through the Organism Selection table when generating a protein for a DNA or RNA sequence.
• The 300 numeric identifiers for the publication information are displayed after the 200 numeric identifiers for sequences containing the publication information in a generated sequence listing in PatentIn 3.2 version 3.2.3.
• Everything between numeric identifiers <210> and <400> are removed for any skipped sequences from a generated sequence listing in PatentIn 3.2 version 3.2.3.
• The separator is changed from "and" to " + " to separate multiple files in a single import in PatentIn 3.2 version 3.2.3. Spaces on either side of the plus sign are mandatory if the user types this in (Most users will use multiple selections in the Import dialog to achieve this and will not notice the change).
• PatentIn 3.2 version 3.2.3 accepts pathnames with imbedded spaces when import files.
• The default folder is set to the user's personal folder for operating systems subsequent to Windows XP in PatentIn 3.2 version 3.2.3.
• The user manual has been updated for PatentIn 3.2 to reflect the new features added to PatentIn 3.1.

Key enhancements over PatentIn 3.1 included in PatentIn 3.2 version 3.2.2:

• PatentIn 3.2 can create default explanations for "n"s and "Xaa"s in the sequence listing that have no user-supplied explanations. The default explanations take the form of misc_features containing the location of the variable characters, and the message, "n is a, c, g, or t" for nucleic acid sequence or "Xaa can be any naturally occurring amino acid" for protein sequences. There is a check box on the main screen entitled, "Check for missing misc_feature" that can be used to turn this feature on or off. Users may wish to check the box and press Validate to see if there are any variable characters not defined by a misc_feature. If the box is unchecked, PatentIn 3.2 will create any missing misc_features. Users may create selected definitions by hand and PatentIn 3.2 will provide the remaining ones.
• PatentIn 3.2 has a character filter, also controlled by a check box, that will import text files of sequences that contain characters other than nucleotide or amino acid symbols such as spaces and numbers. When the box is checked, PatentIn 3.2 will import recognized symbols and omit unrecognized ones. Otherwise, unrecognized symbols are considered an error, and the sequence will not be imported. This is the same filtering function that was performed by PatentIn 2.1, now present in PatentIn 3.2.
• Patent 3.2 allows the user to apply a comment for all artificial/unknown sequences that do not already have a comment.
• These extra features, we believe, will lessen the time that was required to manually provide each and every definition for a variable.
• PatentIn 3.2 permits the user to import a Protein/3 file without a header.
• The user manual is not being updated at this time; all previous functionality of PatentIn 3.1 remains intact. A supplemental user manual explaining the new features is available for download. The contact information (below) is also unchanged.
• PatentIn 3.2 has been tested and certified to run on Windows XP.

Key enhancements over PatentIn 3.0 included in PatentIn 3.1:

• In PatentIn 3.0 when entering data on screens that have an "Insert" button. It is necessary to press Insert after entering data in order to properly insert data into the table. Failure to do so would result in loss of the data. In PatentIn 3.1 pressing OK is equivalent to pressing Insert and then OK if the selected feature is different.
• In PatentIn 3.x multiple sequences may be imported from a single file by using a header line stating: <SequenceName;SequenceType;OrganismName>. In PatentIn 3.1 single sequences may be imported from a single file without the header.
• Where a nucleic acid sequence contains "n" in a coding sequence and a CDS is used; the "n" is defined by selecting "misc_feature" from the drop-down list. PatentIn 3.0 would repeat this feature section for the supplemental amino acid sequences that are automatically generated. This required the user to manually edit the sequence listing to provide a definition for the Xaa thus generated. PatentIn 3.1, however, goes a step further and automatically provides the definition of the resulting Xaa as whichever amino acids correspond to the codon in which the "n" occurs. Thus, PatentIn 3.1 will insert fields <220> through <223> into the generated supplemental protein sequence, which will contain the automatically generated definitions.
• The length of the sequence length that PatentIn 3.1 can handle is solely determined by the machine; there is no built-in limit. PatentIn 3.0 could handle sequences containing up to about 2 million bases, PatentIn 3.1 can handle up to about 4 million bases.
• Patent 3.1 corrects the behavior of PatentIn 3.0 regarding enforcement of a definition for each and every "n" in a nucleotide sequence and each and every Xaa in a protein sequence.
• PatentIn 3.0 did not correctly display split codons when the exon feature was used. This has been corrected in PatentIn 3.1
• PatentIn 3.1 permits the definition for the protein sequence type to be other than "Protein/1". Entries such as PRT1/, prt1, prt/1 and PRT/1 are recognized. This is to make PatentIn 2.1 users more comfortable and allow for common typographical errors.

Key advantages of PatentIn 3.1 over PatentIn 2.1:

• Processes large sequences (over one million bases) and applications with a large number of sequences (over 100,000).
• Imports multiple sequences from a single file.
• Imports multiple sequences from multiple files as well.
• Features defined for nucleic acid sequences are carried over to the supplemental amino acid sequences generated by the CDS feature.
• More user-friendly as the design follows standard Windows user interface conventions.
• Looks and feels more like other Windows-based programs.
• Projects are portable from one computer to another provided PatentIn 3.1 is installed on each workstation.
• Overall lines of code have been reduced to 25 percent of that required by PatentIn 2.1.
• Easier to modify and maintain code written in Visual C++.

System Requirements

PatentIn 3.5 is certified for Windows XP and Windows Vista. A minimum of 512 MB of memory is recommended.  For the best performance 1 GB of memory may be required for larger sequence listings (see Hints below). The disk space required to install PatentIn 3.5 is 6.5 MB. Additional disk space is required to store project files and sequence listing files.

Installation Instructions

Download PatentIn 3.5 onto your computer using the link below. Before the installation, be sure to close all running applications on your computer. Although PatentIn is designed to preserve previous environments, it is always appropriate to back up your previous sequence data before installing a new version. Double-click on the PatentIn35.exe file, which begins the installation. In order to install PatentIn 3.5 software, you need Local Administrative privileges. Follow the instructions given by the setup program. Start PatentIn 3.5 by double clicking on the PatentIn 3.5 icon, which the setup program placed on your desktop.

PatentIn 3.5 was not designed to be installed on a network server, each workstation must have it installed individually. This is because there are "parts" that must be registered on each machine. Project files and sequence listings may, however, be saved to a network server. The most recent Save Project command sets or resets the default.

Hints for Ease of Use of PatentIn 3.5

• Select the third radio button “From PatentIn Generated ST.25 Sequence Listing File” and select a file name on the Import Sequence(s) screen when importing a PatentIn-generated ST.25 sequence listing file.  The selected file name should have “_ST25.txt” at the end of the name, for example, DemoSeq_ST25.txt.
• When importing multiple sequences from a Non-ST.25 single file each sequence must be preceded by a header line stating:

< SequenceName;SequenceType;OrganismName>

See User’s Manual, Section 5.3.1.1, for explanation of terms.

• Do not use both Exon and CDS in the same region of a sequence (i.e., bases designated as the Exon and CDS start and stop should not overlap). PatentIn 3.5 gives precedence to the CDS feature so the exon feature is effectively ignored.
• Use mat_peptide only with CDS, never with Exon. If CDS regions are defined within exons and the mat_peptide feature is used, PatentIn 3.5 is not able to track the amino acid numbering between the CDs border and the exon border.
• If your sequence listing has very long sequences or a large number of sequences, some of the processes in PatentIn 3.5 will take more time to execute and tie up more of the computer's memory. Using a higher-end computer with more power and speed will minimize these problems.
• When you close PatentIn 3.5, it needs to delete TEMP files and clear the memory. If your sequence listing is large it can take some time to accomplish this. One consequence of this is that, if you close PatentIn 3.5 and discover that you forgot to include something, you will be unable to reopen the program immediately.
• If a feature other than "misc_feature" is used to define an "n" that occurs in a coding region, the feature section will not be repeated in the supplemental amino acid sequences, which will thus lack a definition for the Xaa generated by the CDs feature. Thus, the sequence listing will not be in compliance.
• PatentIn with versions prior to PatentIn 3.4 is packaged with a Microsoft Access program, patin2xconvert.mdb, that contains links to the standard database files that PatentIn 2.1 uses. In order for PatentIn with versions prior to PatentIn 3.4 to import PatentIn 2.1 projects, Microsoft Access97 must therefore be installed. Please see Appendix J of the User’s Manual for more information like this.
• The Copy-to-Disk function in early versions of PatentIn was reported to not always perform correctly. Occasionally, the sequence listing copied onto the disk will be missing some hard returns and several numeric identifiers would appear on the same line. This can be easily detected by running Checker on the sequence listing on the disk.  The latest versions of PatentIn 3.x now do their own word wrap, which we believe should eliminate the problem. However, if this problem reoccurs, reopen PatentIn, regenerate the sequence listing, and copy the sequence listing to disk via Windows Explorer.

For help related to downloading the application or using PatentIn 3.5 to report problems encountered running the program call toll-free to

The Patent Electronic Business Center at (866) 217-9197

or contact them via Email at EBC@uspto.gov

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