ESTplus, an integrated software tool collection, was developed to support better project management and provide more comprehensive collection of analysis tools. ESTplus allows its users to manage, create, modify, and remove EST libraries from their own projects. It consists of public programs necessary for performing a traditional EST analysis: sequence cleansing, clustering and assembling and annotating. In addition, the system was enhanced from other EST databases by including additional modules to help identifying functionally-significant or rare sequences as the following. First, library comparative analysis module finds the association between genes among EST libraries according to Gene Ontology (GO) terms using chi-square test (X2). Second, integrative proteomics and EST data analysis module reversely identifies EST sequences that correspond to a short amino acid sequence resulted from a proteomic experiment. Third, a primer design module guides primer selection from gene contigs and/or sequences from the EST data. These enhanced features allow the better and easier utilization of the available EST data for functional genomics and translated biological research.
- Eakasit Pacharawongsakda, Sunai Yokwai, Nitsara Karoonuthaisiri, Duangdao Wichadakul and Supawadee Ingsriswang, â€œESTplus: an integrative system for comprehensive and customized EST analysis and proteomic data matching â€œ, Proceedings of the 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE2008: http://www.icbbe.org/), May 16-18, Shanghai, China, pp. 29-32, ISBN: 978-1-4244-1747-6.
Key features of ESTplus:
- Providing both predefined typical and customized pipelines for EST analysis.
- Trimming or masking low-complexity, repeat and contaminant sequences in EST sequences.
- Clustering and assembling EST sequences into contigs and singletons.
- Sequence annotation using four integrated tools: BLAST, BLAST2GO, InterProScan and TargetIdentifier
- Providing the library comparative analysis module (identification of rare library-specific genes according to Gene Ontology (GO) terms).
- Translating proteins to EST sequences.
- Predicting full length genes
- Designing the PCR primers