GeneDirectory functions

Multi-user

As with all Syngene software, GeneDirectory can be set up for multiple users, with database and display preferences fully customisable for each individual.

Unlimited storage

GeneDirectory has the potential for storing an infinite number of databases. The only limit to the size or number of databases is the size of the storage system - hard disk, zip drive, server, etc.

Using the standard Windows Explore method, users can view the 'tree structure' of the database, easily positioning gel data using simple 'drag and drop' techniques. Typically the user would file data in a number of folders which may be based on Department, Location, Experimental type. Within these folders, experiments can be stored, each containing complete sets of track data from one or more gels. Since there are no restrictions to the labelling of the database structure, each user can create an unlimited number of databases, folders and experiments.

Versatile comparison facilities

Once classified, it is possible to collate track data in Libraries within the database. Comparison Sets can also be constructed from tracks taken from any experiment, Library or gel. Again these are stored within the database structure.

Intuitive interface

GeneDirectory displays the selected track data in a single window so that the current analysis is always visible, without the need to keep switching to alternative views. Once an experiment, gel, Comparison Set or Library has been selected, a single click produces the display window. This contains the 'gelstrips' (track images) of each track alongside a databox containing detailed information for each track, such as genus, strain and batch. The databox also shows experiment, description and gel ID.

Cluster analysis

This is the most important and by far the most outstanding feature of GeneDirectory. The software has the ability to perform a cluster analysis on an unlimited number of tracks, selected by the user. Any experiment, gel, Library or Comparison Set can be used as the basis for performing a cluster analysis or band match, with a single click. Using Comparison Sets for analysis is very useful when you need to compare results using different primers or restriction enzymes.

The following options can be chosen from a simple set-up dialog box:

Matching type
Match all tracks to each other or match to a single reference
Matching basis
Match by MW, position, Rf
Profile matching
Matching tolerance
Set a percentage for correlation
Similarity Coefficient
Jaccard or Dice (Nei and Li)
Cluster type
UPGMA, UPGMC, Neighbour Joining, Wards, WPGMA, WPGMC, Single Linkage, Complete Linkage

Once selected, a cluster diagram is drawn alongside the 'gelstrips' and databox in the single window display. Naturally, full printing facilities of the results and diagram is provided.

Bootstrapping

This is a resampling technique aiming to indicate the reliability of the cluster pattern in a dendrogram.

Searching (or identification)

One of GeneDirectory's most powerful features is its ability to search for unknown band patterns. There are options to search the complete database or limit the search to defined Libraries, experiments or Comparison Sets. There is no limit to the number of patterns that can be searched at one time.

To further enhance the searching process, patterns can be identified by MW, Rf or Position. The number of results displayed can be set to any number from 1 to 100 and the degree of tolerance (similarity) can be defined. Once these parameters have been chosen, GeneDirectory will quickly display a list of similar patterns showing the number of matching bands. It then displays all the data found (regardless of the original number set) in the single window display along with the track databox. Completing the process is then a simple matter of performing the cluster analysis function again.

Data sharing

Any of the information within the database can be copied to disk or sent via a network or Internet connection. Therefore, provided all users are running GeneDirectory on their PCs, data can easily be shared between colleagues or collaborating laboratories.