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PatentIn version 3.3

PatentIn 3.3 is a computer program designed to expedite the preparation of patent applications containing nucleic acid and amino acid sequences. PatentIn 3.3 generates sequence listings that comply with all format requirements specified in the World Intellectual Property Organization (WIPO) Standard ST.25.

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.

Enhancements:

PatentIn 3.3 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 3.3 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 3.3.
Everything between numeric identifiers <210> and <400> are removed for any skipped sequences from a generated sequence listing in PatentIn 3.3.

The separator is changed from "and" to " + " to separate multiple files in a single import in PatentIn 3.3. 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 3.3 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.

PatentIn 3.3 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 3.3 will create any missing misc_features. Users may create selected definitions by hand and PatentIn 3.3 will provide the remaining ones.

PatentIn 3.3 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 3.3 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.

Patent 3.3 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 3.3 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.

In PatentIn 3.3 multiple sequences may be imported from a single file by using a header line stating:
PatentIn 3.3 has been tested and certified to run on Windows XP.

System Requirements

The system requirements for PatentIn 3.3 are the same as for PatentIn 3.2. It is certified for the Windows 95/98/NT/2000/XP environments but also works in Windows Me. A minimum of 64 MB of memory is recommended for smaller projects. Otherwise 128 MB is recommended. Memory greater than 128 MB may be required for larger sequence listings (see Hints below). The disk space required to install PatentIn 3.3 is 5.9 MB. Additional disk space is required to store project files and sequence listing files.

Installation Instructions

Download PatentIn 3.3 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 PatentIn33.exe file, which begins the installation. In order to install PatentIn 3.3 software, you may need Local Administrative privileges to install PatentIn 3.3. The installation application may not be able to write to the registry or “Program Files” directory due to security constraints implemented on your computer. For example, the shortcut Icon for PatentIn may not be created on the Windows 2000 Platform if you don’t have Local Administrative privileges. Follow the instructions given by the setup program. Start PatentIn 3.3 by double clicking on the PatentIn 3.3 icon, which the setup program placed on your desktop.

PatentIn 3.3 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.