- I know very little about bioinformatics will I be able to use BioNavigator?
BioNavigator has been designed by bioscientists for bioscientists. One of the main benefits of using BioNavigator is its user-friendly and accessible user interface - if you don't know how to use part of BioNavigator or a particular program just click on the Help button. Also, the Protocols section can guide the new user, or a researcher wanting to perform an unfamiliar or infrequently used analysis to a successful outcome. BioNavigator tries to ensure, as much as it can, that the analyses you select to run are appropriate for the data you have.
Take the short tour for a quick overview or for a more in-depth introduction to BioNavigator, download the Tutorial for a step-by-step guide through some practical examples.
- What will the next developments be with BioNavigator?
It is our aim to provide you with access to the most comprehensive range of bioinformatics tools possible. Longer term, we plan on entering strategic partnerships with a number of companies to ensure users can stay apace of the incredible growth of genetic and proteomic information. We are interested in your feedback so if there is a particular feature or function that you would like to see added into BioNavigator, let us know by emailing us at
- Who wrote all the programs in BioNavigator?
The R&D team at Entigen have gathered together the best programs and packages from many sources, predominantly academic but also commercial. These are supplemented by programs written in house at Entigen, where the assorted programs are brought together into an accessible and comprehensive form by the programming team.
- Exactly what programs are available on BioNavigator?
The life scientists who have designed BioNavigator have searched the world to bring together the most complete list of analytical programs available through the Internet. BioNavigator provides access to more than 140 analytical programs (for full details of these programs, see the BioNavigator Program Index) with more to be added in future. Features of the BioNavigator system include functions in the following areas :
- Gene detection and translation
- Molecular evolution
- Molecular modeling
- Motif and pattern analysis
- Multiple sequence analysis
- Nucleic acid structure and analysis
- Pairwise sequence comparison
- PCR primer design
- Sequence family construction and searching
- Protein structure and function
- Sequence database similarity search
- Sequence file management
- Statistical analysis
- How do I cite BioNavigator in my upcoming publications?
When citing your Bioinformatics package in your Methods, please use the following wording:
"Bioinformatics analyses conducted on BioNavigator.com provided by Entigen Corporation."
- Work Bench is your starting point.
When you log in, Work Bench is your first port of call, allowing you easier access to the functionality of BioNavigator. From Work Bench you run programs directly by pasting input sequences or a list of database accession numbers, viewing a database record and/or selecting a file from your account.
You can also access from Work Bench (as well as anywhere within BioNavigator) the main sections of BioNavigator: File Manager, Text Search, Notify, Program Index and Protocols as well as Support, FAQ, online Help, information on your account and submit Feedback.
- What Molecular Modeling programs are available?
Molecular Modeling capability has been incorporated into BioNavigator. ICM and WHAT IF have been used to enable the user to find theoretical models for their protein sequences and engineer their proteins in silico.
- Are there any new Protocols in BioNavigator?
Several new Protocols have been added to BioNavigator and new Protocols will continue to be introduced. New Protocols have been introduced in Phylogenetic Analyses: Protein Parsimony and Protein Distance Matrices; Protein Modeling: Molecular Modeling Homology Modeling, Protein Engineering, Contact Analysis.
- What is the Show History function?
BioNavigator records the steps in each analytical pathway. Click the Show History button for a graphical representation of all the files that are directly and indirectly related to your file including the programs and program options used. This allows you to see where you file came from and what you did with it. You can then select an analytical pathway(s) and save this as an automated Protocol or Macro. This allows you to replicate your own customized analyses on future datasets.
- What are Macros and how can I create my own?
A Macro is an Automated Protocol or a series of analytical steps through programs (including option settings) that allow you to replicate customized analyses at any time on future datasets. Simply select the desired Macro (from Program Index or Protocols) then the appropriate input file(s) or set(s) and click RUN.
You can create you own Macros using the Show History button.
- Sets allow High Throughput analysis
In BioNavigator you now have the ability to create and analyze data in sets. This allows you to batch program runs of up to 10,000.
- What are sets and how do I create and manage them?
A set contains more than one of the same type of file (any file). This allows you to perform the same analysis on many files or batch program runs. You can create a set from individual files using the program Create Set or from two or more sets using Union and Intersection. You can upload multiple sequences in fasta format to create a set. Sets are also created as output files from several programs e.g. saving BLAST hits or a Text Search result.
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