GeneToolKit Manual
Developed By Michael MacDougall
Introduction
GeneToolKit is a tool that allows the user to compile a list of sequences, generate a FASTA file, and perform a multiple sequence alignment of the generated FASTA file.
This multiple sequence alignment can then be sent via Email in ALN format.
This toolkit will offer users a far more convienient and simple interface to perform research anywhere with an active internet connection.
Features
- FASTA Generation
- Header and Sequence Editing
- Sequence Specific Notes
- ClustalW Integration
- FASTA Export via Email
- ALN Export via Email
- Phylogenic Tree Information
- Simple Graphical User Interface
How-To
When GeneToolKit is first launched the user is presented with a two-tab interface with the Sequences tab selected by default.
From the Sequence List tab the user has ability to view, edit and add desired sequences.
Adding Sequences
In order to add a sequence the user must press the '+' button on the top-right corner of the screen and then is presented with the Add Sequence screen.
Two options are available at this point: querying the NCBI database using an accession number and entering a sequence manually.
After the information is entered correctly tapping the 'Add Sequence' button will close the current screen and return the user to the main Sequence List tab.
Emailing FASTA
After adding desired sequences, the user can press the 'Email FASTA' button in the top-left corner and an email message will appear with the FASTA file automatically attached.
Multiple Sequence Alignment
Once the desired sequences are added to the Sequences the user can select the ClustalW tab to align all sequences.
After a few seconds, the resulting multiple sequence alignment will appear in the window along with the phylogenic tree information.
Emailing ALN
After performing a multiple sequence alignment using the ClustalW tab, the user can then press the 'Email Alignment' button to open up a blank email with the alignment attached.
Technical Details
Data Model
The data model consists of a Singleton manager that contains a NSMutableArray that allows for global access using Apple's Grand Central Dispatch (GCD) as a mediator.
The NSMutableArray holds a custom Sequence object that holds the name/accession numner, the FASTA header information, sequence, and sequence-specific notes.
Sequence Retrieval
The sequence retrieval used on the Add Sequence screen is provided by the TogoWS: REST service located at: http://togows.dbcls.jp/site/en/rest.html
ClustalW Integration and Phylogenic Tree Information
The ClustalW integration and phylogenic tree information is provided by MSU's Genebee.
A POST method is used with a NSMutableURLRequest to retrieve the data.
The data is then displayed in a UIWebView to allow for HTML styling and formatting.