BioNumerics Plugin Tools

Miscellaneous tools  Clone experiment type Tool to clone an existing experiment type, i.e. to create an identical experiment type with a different name. For Fingerprint types in particular, this tool can be convenient. For example, in case multiple restriction enzymes are used in combination with the same reference pattern, one fingerprint type can be cloned to obtain a second without having to re-enter the reference positions and other settings. The tool also works for character type data and sequence type data. The script asks to select an experiment type to clone from a picklist, and provides an input box to enter a name for the cloned experiment type.  Character statistics Tool which provides some statistics on character type data. The script prompts for a character type from the database, and then creates a tab-delimited list with some statistics on all the characters: they percentage of entries for which the character is present (a zero value does not mean the character is absent), the percentage entries where the character has a positive value (different from zero), the average value over all the entries, and the standard deviation on the character's average value. The table can be copied into a spreadsheet.  Create ARDRA profiles Tool to create synthetic ARDRA profiles (Amplified Ribosomal DNA Restriction Analysis) based upon sequences and a selected restriction enzyme. The script prompts for a sequence type to use as input (usually ribosomal DNA sequences), and a fingerprint type to store the profiles in. Make sure a fingerprint type is present that has the right range in bp. The fingerprint type is by preference generated based upon a real electrophoresis experiment. When doing so, artificial gels patterns be compared with real patterns resulting from ARDRA cleavage experiments. However, a fingerprint type with a specific MW range can also be geterated using a theoretical logarithmic curve (see manual). The script also prompts for a restriction enzyme to use. Note here, that more than one enzyme can be selected to create mixed cleavage fragments. The user should also enter a starting primer sequence and an ending primer sequence. This is very important in order to trim the artificial patterns to the same length, and to make them compatible with your own experimental results. A number of mismatches can be allowed. Finally, a name should be entered for the gel file (Output file name) and a resolution value for the generated densitometric curves. NOTE: the tool needs a data file restr.txt which should be present in the home directory of the software (usually c:\Program files\BioNumerics\Data).  Find and update MLST alleles. Tool to determine alleles for Multi-Locus Sequence Typing. The script requires a character type MLST to be present in the database. When executed, it prompts for one or more sequence types to be processed (multiple sequence types can be selected). After clicking OK, it will prompt the user for each new variant found to add it or to ignore it. There is also an option Add all. The alleles found are stored in a file MLST.TXT in the database directory. The character type MLST is updated with new allele lnumbers and the characters are filled for the entries.