ESTExplorer

ESTExplorer performs pre-processing, clustering, assembly, conceptual translation, and nucleotide- and protein-level functional annotation of expressed sequence tag (EST) datasets.

Key Features:

• Distributed Control Approach: Employs a distributed control methodology using dedicated processors to run selected bioinformatics programs across EST-analysis stages.
• Species-Specific Repeat Masking: Implements species-specific repeat masking during preprocessing to reduce repetitive-sequence artifacts.
• Conceptual Translation: Performs conceptual translation to derive putative protein sequences from ESTs or contigs.
• Input Format and Program Selection: Accepts ESTs in FASTA format and supports selection of specific analysis programs.
• Pre-processing and Assembly: Includes pre-processing and assembly steps and accepts preassembled contigs for downstream analysis.
• Functional Annotation: Annotates sequences at nucleotide and protein levels, producing gene ontology assignments and protein functional identifications mapped to domains and metabolic pathways.
• Individual Sequence Analysis: Supports individual analysis of functionally annotated contigs and ESTs.

Scientific Applications:

• Parasitic Nematode EST Annotation: Applied to annotation of large EST datasets from parasitic nematodes to identify novel genes and potential targets for parasite intervention.
• Gene Discovery and Transcript Analysis: Supports gene discovery, transcript analysis, and functional annotation of putative gene products in genomic and transcriptomic studies.

Methodology:

Distributed control using dedicated processors to run selected bioinformatics programs; computational steps explicitly include pre-processing, species-specific repeat masking, clustering, assembly, conceptual translation, database matching, and functional annotation.