PatentIn instructions and software

PatentIn Version 3.5.1 Software is available for free download:



Hints for Ease of Use of PatentIn 3.5.1

  • 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, 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 3.5.1 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 3.5.1 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 3.5.1 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 3.5.1, 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 3.5.1 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.


Where to Call for Help

For help related to downloading the application or using PatentIn 3.5.1 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