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Gene Inspector® is a unique combination of a versatile electronic laboratory research notebook, a comprehensive sequence analysis product, and a powerful Illustration tool. This electronic notebook will allow you to plan, organize, and carry-out your experiments and analyses in such an innovative way that you will never want to go back to the way you are doing it now. The Gene Inspector can perform many sophisticated DNA analysis and protein analysis tasks, but this software is much more than just another sequence analysis product. Imagine having the ability to define an entire suite of analyses to be performed each time you have a new sequence, and to design custom style sheets which specify exactly how your output will look for each analysis. Because you can predefine and store analysis parameters for any DNA sequence analysis or protein sequence analysis to fit your needs, anyone in the lab will be able to obtain meaningful and consistent results, whether they are a novice just entering the lab, or an experienced researcher familiar with the analysis routines. The combination of an electronic notebook with navigation and drawing tools and sophisticated analyses provides the ability to annotate experimental results and analyses in a single location, rather than keeping your sequence analyses separate from you lab notes.
Gene Inspector was designed from ground up to work the way you naturally work as a biologist – you are not constrained by the structure of the program to perform tasks in a predefined way.
Gene Inspector is centered around a powerful notebook that serves not only as a container for analysis output but as a genuine laboratory notebook and illustration tool. The Gene Inspector Notebook can contain information or annotations that you previously kept in your old fashioned paper notebook along with all your sequence analysis and laboratory experimental results. Why keep these two parts of your research artificially separated when you can combine them in a single location?
Gene Inspector has built in hotlinking, which allows you to connect a sequence to a set of analysis routines. Each time the sequence is changed, the output results can be set to be automatically updated.
All analyses run in background so you can continue to work in your notebook or even in other programs without interrupting the progress of the analysis.
Gene Inspector contains analysis suites, which provide a way to create a collection of analysis routines and associated parameters that meet your needs.
Analysis suites can be recalled by selecting them from a menu and specifying a sequence (or several sequences) to be analyzed. This provides consistency and allows even beginners to produce results that can be compared directly with those of more experienced users in the group.
Gene Inspector contains interactive analysis output objects that allow you to fine tune analysis results to examine exactly what you are interested in.
Gene Inspector Notebook sheets can be adjusted to any size – great for designing posters, slides, or just making the notebook fit your screen - text automatically reformats to fit the notebook size.
Gene Inspector Notebook appendices can store commonly needed information (like buffers, vector descriptions, etc.) which can be viewed at any time from any location in the notebook. Gene Inspector provides over 60 different nucleic acid and protein analyses including: sequence alignment, base composition/distribution, ORF determination and evaluation, restriction mapping, sophisticated multipartite find, dot matrix comparisons, antigenicity, hydropathy, transmembrane helices, helical wheel, Prosite motif searching, physical characteristics, signal sequence, protein structure prediction, and many more. Many analyses can be done using median sieving to bring out structures of a specific size (i.e. -membrane spanning)
Gene Inspector allows you to easily navigate in the notebook through electronic bookmarks and aliases. Gene Inspector Notebook extension are instantly available with the click of your mouse button and can contain formatted table templates, analyses, graphics or text that you use often.
The Gene Inspector® Advantage: Combining sequence analysis and an electronic notebook in one application. All Laboratory Notes Are Kept in an Electronic Notebook
Scientists perform experimental bench research using gels, columns, PCR, etc. on DNAs they are interested in studying. Notes are taken in a lab notebook. Often the same sequences are being studied in a sequence analysis package that may allow the user to save analysis results one window at a time. This often leads to collections of paper output from the analysis program that are cut and pasted into the paper lab notebook or else stored separately. This is not the best way for researchers to work. In the Gene Inspector, all laboratory notes are kept in an electronic notebook, which also serves as the site for all the sequence analysis results. Thus, the entire project – both sequence analyses and experimental results -- are stored in a single location. There is no artificial separation of analyses and discussion of experimental results.
Track Projects Using Bookmarks, Appendices and Aliases
Bookmarks, appendices and aliases provide a convenient way to track different aspects of the same project and navigate within the GI notebook. Bookmarks can take a user to any location in the GI notebook instantly -- such as different experiments, a specific date, a page of buffer recipes, etc. Appendices are like appendices in a book and are accessible through a menu item. An appendix is opened in its own window (which is still part of the notebook) and can display often used information -- like an annotated sequence, a restriction map, experimental protocols, etc. Aliases function like aliases in the Macintosh Finder. An alias can be created to any object (including an appendix) and then the alias can be moved to any location, even to a different notebook. When the alias is double-clicked, the user is taken to the object pointed to by the alias; if the alias points to an object in a closed notebook, that notebook is opened and scrolled to the appropriate location. These enhanced and very natural navigation tools provide the user with a significantly more effective research notebook environment than their current paper notebooks.
Use the Gene Inspector Notebook as a Presentation Tool
The Gene Inspector notebook is designed to serve as more than just a repository for information. Because the Gene Inspector notebook can be resized and the layout easily changed, the Gene Inspector notebook can be used directly to generate posters, slides, and other illustrations for seminars and lectures. The background Gene Inspector notebook text can be "styled" as conditional text and then either shown or hidden. Thus, only the text you want to see will be shown when making the illustration. This enables the Gene Inspector notebook to serve as a daily workbook and also to be used as a presentation tool.
Hotlink an Analysis to a Sequence
Often a researcher will be working on a sequence that is constantly being refined. As new information about the sequence comes to light, there is a need to repeat all the analyses based on that sequence. The Gene Inspector has the ability to hotlink an analysis to a sequence. This means that when a sequence is changed, all dependent analyses can be updated automatically. There is no need to go back and define parameters and start the analysis again.
Define and Save an Entire Suite of Analyses
By changing the parameters used to run an analysis it is possible to get very different results. Thus, different researchers in the same lab might get results that cannot be compared realistically -- and they might not even realize the problem. The Gene Inspector allows users to define and save an entire suite of analyses with all associated parameters. Any user in a group can then choose the suite from a menu and perform analyses on new sequences and obtain directly comparable results. Therefore, the Gene Inspector’s analysis suites can provide a consistency never before available -- making for more meaningful sequence analyses.
Other features in Gene Inspector®:
BLAST Search Directly from Gene Inspector
Performing a BLAST search of GenBank over the internet directly from within Gene Inspector. This is launched exactly the same way other analyses are launched. Just to choose a sequence from GI, set any BLAST parameters, and then run the analysis. Your analysis setup including all the BLAST parameters can be saved for other users to use. Save one setup for finding only very close matches, and another one for finding distant sequence relationships.
Perform Multiple Analysis & Show Sumary Results!
A number of analyses can be performed and summary results shown. This will create a single output object in the notebook that has a result for each sequence in the analysis. Double-clicking on the single sequence result will allow you to launch the complete analysis of that sequence.
Add Sequences to the Analysis Setup Panel
Sequences can be added to the analysis setup panel by selecting a sequence file that contains multiple sequences - all sequences in the file are then added to the analysis panel.
sequences can be added to the analysis setup panel by selecting an entire folder - all sequence files in that folder and all subfolders will be added to the analysis. This is very useful for searching for a specific sequence.
Drag & Drop Between Many of Your Favorite Applications
Extensive Drag & Drop options are available allowing objects to be dragged between GI windows and also between GI and other Drag & Drop enabled applications. For example, you can drag an analysis result or a multiple sequence alignment directly from Gene Inspector to Adobe Photoshop or Illustrator, or to Microsoft Powerpoint or Word.
640 Different Ways of Displaying Multiple Sequence Alignments
There are now over 640 different ways of displaying multiple sequence alignments. You can show characters that match (or don’t match) the consensus, you can invert character appearance, shade matches, box them, color the background behind characters that match or don’t match the consensus, etc.
We Understand Your Need for Speed
Many Gene Inspector routines have been rewritten for speed
Don’t Want to Leave GI But Need to Do a Quick E-mail Check?
You can send messages and check e-mail from within GI
Creating Posters and Slides on the Fly!
You can drag a multiple sequence alignment from the sequence window directly into the GI Notebook, where you can alter the display of the alignment. This is useful for creating posters and slides because the multiple sequence object in the notebook can be shown in relation to other analysis objects in the GI notebook and adorned with arrows or other graphic objects.
