Gene Sequence Management (GSM)
ISL has developed a web-based phylogenetic analysis pipeline and database management system, named as GSM, for automating the workflow of sequence-based identification. GSM integrates a set of phylogenetic software with in-house and public database. The GSM system was designed and implemented using free software, for example, MySQL as storage for sequence, Bioperl objects as pipeline for analysis software, and PHP and Java scripts providing the web interfaces for data access, navigation and visualization.
- S. Ingsriswang*, S. Yokwai, C. Sriwiroj, W. Potachareon (2004). GSM: A web-based phylogenetic pipeline and database management system for microbial identification, Proceedings of the Tenth International Congress for Culture Collections Tsukuba, Japan, 10-15 October, 472-473.
Key features of the system include:
- Sequence search using Blast with BIOTEC (only microbe available) and GenBank database,
- Sequence selection from the Blast output and Sequence Retrieval from the database for further analysis,
- Multiple sequence alignment using ClustalW performed on the selected sequence from the Blast output,
- Multiple sequence alignment view using JALVIEW,
- Phylogenetic tree construction using available methods from the PHYLIP package executed on the ClustalW output,
- File format conversions, and
- Basic statistics information for each sequence entry is also provided, for example, GC content, number of codons used, and molecular weight.
In addition, scientists can directly cut and paste or upload their own sequences to do only the preferred analysis.