Skip to main content
hpa logo
Topics A-Z:
Search the site:
Home › Products & Services › Infectious Diseases › Services and Activities › Bioinformatics ›Resources ›  Bioinformatics Scripts
Printer friendly page (opens in new window)

Bioinformatics Scripts

Scripts can provide many additional functions can be as simple as automating current repetitive tasks e.g. renaming multiple files, and can extend to projects as large as identifying genes in microbial genomes. Many of the larger programs commonly used by biologists today started as scripts, which then grew alongside the research they were designed to assist.

Please note: The scripts provided on this website are not supplied with any guarantee or admission of liability from the HPA Bioinformatics section. We also cannot guarantee the quality of scripts available from linked sites. Any loss or damage resulting from the use of these scripts is the sole responsibility of the user.

Friendly Advice: Read any installation or operating instructions carefully before installing/executing a script. It is also advisable to backup any irreplacable data.

BioNumerics Scripts

BioNumerics is possibly the most widely used biological analysis package in the HPA. One of the reasons for this is the ability to customise the program via the inbuilt scripting language.

 

HPA Developed Scripts

The Bioinformatics section generates scripts in response to specific queries from users. Scripts that are then deemed to be of wider use are rendered into a generalised format and made available.

HPA staff can request script alteration or generation of a novel script by contacting bioinformatics@hpa.org.uk

Please download and read the README files before installing or running these scripts

  • Convert Binary to Hexadecimal or Octal (Text Document, 7 KB)


    The recommended notation for spoligotyping data is now a hexadecimal or octal format ( reference paper). This script will convert the standard 43 point binary spoligo output into one of the recommended formats, and store the results in a named database field.
    Please read before running this script. README (PDF, 38 KB)

      
  • Database Backup (Text Document, 1011 byte)


    This script will automatically create a backup of a BioNumerics database, labelled with the date of backup, and save it to a specified folder. A list of all the files that are being backed up will be displayed as they are being processed.
    This script requires that the programming language PERL is installed on your PC (If you would like PERL installed on your PC, please contact your IT administrator) The Backup script illustrates a very simple but effective way that PERL and BioNumerics can work together, and provides a gentle introduction into the benefits of PERL in general.
    Please read before installing or running this script.   README (PDF, 36 KB)

  • FASTA Sequence Exporter (Text Document, 2 KB)


    This script will take the sequence data for a specific experiment from a number of selected BioNumerics entries, and save it all in a single file in the FASTA format.
    Please read before running this script   README (PDF, 37 KB)

  • Primer Matcher (Text Document, 4 KB)


    This script will take a query sequence and compare it to a predetermined list of primers (both forward and reverse) allowing for a user defined number of mismatches. The output is a text file showing primers that match within the criteria, the location of the primer on the query sequence and the number of mismatches that occur.
    Please read before running this script   README (PDF, 40 KB)

  • Sequence Importer (Text Document, 4 KB)


    This script will take files of sequence data in a given directory and perform one or both of the following functions:
    1. Collect all sequences into a single FASTA format file.
    2. Add the sequences to a Bionumerics database.
    Please read before running this script   README (PDF, 38 KB)

       

 

Online Script Libraries

Disclaimer: The websites whose links are listed on this site are not under the control of the Health Protection Agency which is not responsible for the content of these sites. These links do not serve as an endorsement by Health Protection Agency of any of these sites and they are provided solely for the convenience of our users. Please contact us with the details of any URL changes in the following links
The primary source of BioNumerics scripts is the Applied Maths website. Scripts are categorised by function and are accompanied by brief details of their use.

 

How to install BioNumerics scripts

BioNumerics scripts are very easy to install into any existing BioNumerics setup.

1. To download the script, right-click the link and 'Save target as...'

2. Move the saved script, and any associated files, to the "scripts" folder of your BioNumerics installation

  • This will be 'C:\Program Files\BioNumeric\scripts' for a standard installation.
  • For non-standard installations
    • Open BioNumerics and select 'Edit script...' from the 'Scripts' menu.
    • Select 'Save script' from the 'File' menu in the script editor.
    • The file selection dialog box will open at the 'scripts' folder, and the dropdown menu will allow you to locate it in your filesystem
  1. Change the file extension of the script to .BNS by removing the .TXT if necessary.
  2. Always read the associated README file before running any scripts. It will tell you how to use the script properly and will warn of any potential problems.

The next time that you start BioNumerics the newly installed script will be available via the 'Scripts' menu in the main BioNumerics window.


Last reviewed: 30 September 2008