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.