STORM

(Systematic Tailored Orf-data Retrieval & Management)

 

GoTo PHIRE-program

Please cite:

Lavigne, R., Sun, W.D. and Volckaert, G. STORM towards protein function: Systematic Tailored ORF-data Retrieval and Managment. Applied Bioinformatics (2003) 2(3): 177-179

Questions?

FAQs and discussion

Created at Katholieke Universiteit Leuven, LoGT

Download ver 1.01

Description

STORM combines protein analyses of BLAST, FASTA, Pfam and ProtParam on a batch-file of protein sequences. It subsequently summarizes and organizes the output in an Access database format.

More specifically, STORM extracts protein sequences after ORF prediction and subsequently performs an automatic analysis for each of the proteins. This analysis consists of web-based similarity searches (BLASTp and FASTA) as well as Pfam predictions and Protparam calculations of protein physicochemical properties. The raw output for these analyses is then analysed and summarized. All these steps require a minimal amount of user interaction (ONLY A FEW MOUSE-CLICKS!!!) and all the data is stored in a Microsoft Access database, allowing control over the raw output as well as the summarized information by this program (However, the access database is not strictly required for creating a summary). This program is widely applicable for any set of proteins, but was initially developed primarily to analyse bacteriophage genomes.

The STORM program is a lightweight program, can be active simultaneously with other programs running on the PC and consists of 4 modules (Figure 1). Each of these modules is an independent program, generating an output used in the following module.

Figure 1: STORM program modules

 HowTo:

Below you will find screendumps for the different modules of the program.

 

The gene extraction output can be saved as either a batch-file of DNA sequences or as a batch of protein sequences.

 

After entering the project name and pasting the protein sequences, the user can select which analyses should be run. To start the data retrieval, just press start. The program will notify you when data retrieval is finished. (This time depends on the speed of the webservers

 

.

Raw data output can be viewed as text or in html-format (where available). The raw data records can be edited in this module.

 

The Data Summary module contains record summary from the raw data module when you hit the summary button. Pressing "Save File" will store all records (analyses) on a specific protein in a single txt-file.

 

Microsoft Access

Users with Microsoft Access installed, can access the DB database and have full control over the gathered data. The database consists of various segments as shown in the following picture, to increase flexibility (e.g. change website)

 

WebData and Datasummary contain the retrieved information from the web-servers. Each record consists of multiple field, also increasing flexibility in the organisation of these records..