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Checker Version 4.4.6

Checker Version 4.4.6 is a Microsoft Windows-based software application for checking biotechnology Sequence Listings for compliance with format and content rules. Checker Version 4.4.6 validates sequence listings generated in accordance with the US sequence rules, 37 CFR §§1.821 - 1.825, effective July 1, 1998, the World Intellectual Property Organization (WIPO) Standard ST.25, as well as Sequence Listings created with the “old rules”, those which became effective October 1, 1990.

Checker Version 4.4.6 replaces all previous versions. Checker allows public users to check Sequence Listings in Computer Readable Form (CRF) before submitting them to the United States Patent and Trademark Office (USPTO). Use of Checker prior to filing Sequence Listings has resulted in fewer Sequence Listing errors discovered by USPTO, therefore fewer Sequence Listings returned to Applicants for correction. Checker 4.4.6 features full compatibility with the Microsoft Windows XP, Vista, and 7 operating systems as well as all Office 2000/XP products. Also, a setup file named, Checker.msi , assures fast and easy installation of the application.

 

Please Note: Should an installation path other than the default be specified, the initial execution of Checker will require modifications to the input and output folder paths.  The user will be alerted to this and then presented with the Checker Properties Dialog (see User’s Manual Section 3.2.6).

Checker 4.4.6 Maintenance Enhancements:

The Help file was updated for compatibility with Microsoft Windows Vista and 7.  This was accomplished via recompilation of the help data using an updated version of RoboHelp.

Checker 4.4.6 will give an error message if the last line of an amino acid sequence is not numbered on succeeding line.

Checker 4.4.0 Maintenance Enhancements:

Checker 4.4.0 will give an error message, for numeric identifier <213>, when organism has both "Artificial" and "Unknown" on the same line. The organism field should reflect only one of the following: Genus Species (scientific name), "Artificial Sequence", "Unknown".

NOTE: The USPTO no longer certifies Checker for the Windows environments of 95/98/ME. Testing and support of Checker on these older versions of the Windows operating system has been discontinued.

System Requirements:

The recommended minimum memory requirement for a workstation running Checker Version 4.4.6 is 64 MB RAM plus cache space, which may also expand depending on the input file size. Storage space for the output files will vary according to the size of the Sequence Listing being checked. The user should allow at least 50% additional space for Checker report files.

User Notes:

1.  A macro for use in Microsoft Word which activates line numbering, to enable viewing line numbers in a Sequence Listing, is included with the Checker distribution files and is automatically copied to the Checker installation folder. The name of file is CrfMacros.doc. To access it, open MSWord, select the open file icon, navigate to the Checker installation folder, and select the macro. As an alternative, the user can download a text editor or viewer with line number display capabilities.

2.  Checker does not verify the contents of Other Information fields (i.e. <223>), only that a required comment is present. Such comments include definitions of any "n"s or "Xaa"s that appear in the   Sequence Listing and comments regarding selection of Artificial Sequence or Unknown for the organism. Thus, the user should pay careful attention to the content of these fields.

3.  Checker does not verify that the contents of the organism fields (i.e. <213>) are either a scientific name (Genus species) or the text “Artificial Sequence” or “Unknown”. No other type of entry is permitted as an organism name. Thus, the user should pay careful attention to the content of these fields.

4.  Checker does not indicate the presence of extraneous text at the end of the sequence listing. The end of the sequence listing should be the actual sequence of last sequence record. Extraneous text can be introduced at the end of the sequence listing when a sequence listing file in a format other than ASCII, e.g. a *.doc file, is converted to ASCII file format. For example, a page number or a footer will be inserted at the end of the file if page numbering or a footer was present in the non-ASCII file. Thus, the user should verify that no extraneous text is present at the end of the sequence listing.

5.  Checker does not indicate an error due to the presence of extraneous blank lines that are introduced between a line of nucleotide sequence and a line of corresponding encoded amino acid sequence or between a line of amino acid sequence and a line of corresponding amino acid residue numbering. Extraneous blank lines can be introduced when a sequence listing file in a format other than ASCII is converted to ASCII file format. For example, soft and hard page breaks in a non-ASCII file format are converted to blank lines when the file is converted to an ASCII text file. Thus, the user should verify that extraneous lines are not present in the sequence portions of the sequence listing.

6.  Checker does not verify that individual letters in nucleotide or amino acid residue abbreviations in the nucleotide or amino acid sequences have the proper case. Three-letter amino acid abbreviations must have the first letter in upper case and the remaining letters in lower case. Nucleotide abbreviations must be lower case under the current rules, or upper case under the original rules. Thus, the user should pay careful attention to the case of letters in nucleotide and amino acid residue abbreviations.

7.  Checker does not indicate an error when a termination symbol is present in an amino acid sequence line opposite a stop codon in a nucleotide sequence. Amino acid sequence lines may not contain symbols, e.g. “*” or “Ter”, indicating a termination sequence or stop codon in the corresponding nucleotide sequence. The only text permitted in an amino acid sequence line are those of the amino acid abbreviations. Thus, the user should verify that amino acid sequence lines do not contain characters representing a termination sequence or stop codon.

8. Checker does not verify the term entered following a <212> identifier as the molecule type, i.e. "DNA", "RNA", or "PRT," is in upper case as required.  Thus, the user should pay careful attention that all letters in these terms for molecule type are in upper case.


Download Checker Version 4.4.6 Software (file size 1.33 MB)

 



Where to Call for Help

For help related to downloading the application or using Checker 4.4.6, or 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

United States Patent and Trademark Office
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Last Modified: 11/19/2012 3:19:04 PM