ShrimpGPAT

ShrimpGPAT provides gene and protein annotation for shrimp by aggregating quality-filtered molecular sequences and in-silico functional annotations to support gene discovery and functional genomics.

Key Features:

• Extensive Molecular Sequence Database: hosts quality-filtered molecular sequences from 14 decapod species, including approximately 500,000 records for six penaeid shrimp and eight other decapods, derived from Sanger sequencing and massive-parallel sequencing technologies.
• Functional Annotation and Sequence Analysis: provides in-silico functional annotations based on sequence homologs, gene ontologies (GO), and protein-protein interaction data.
• Sequence Similarity and Alignment Tools: supports BLAST (Basic Local Alignment Search Tool) queries and multiple sequence alignment analyses against predefined databases.
• Community-Based Annotation: records researcher-contributed functional annotations, tags, and comments to augment sequence annotations.

Scientific Applications:

• Gene Discovery: identification of novel genes within shrimp species using aggregated sequence data and homology searches.
• Functional Genomics: exploration of gene functions and interactions through GO annotation and protein-protein interaction information.
• Comparative Genomics: analysis of genetic similarities and differences among decapod species using the multi-species repository.
• Aquaculture Enhancement: generation of genomic insights to inform shrimp breeding and cultivation strategies.

Methodology:

Integrates sequence homologs, gene ontologies, and protein-protein interaction data to predict gene functions, and employs BLAST and multiple sequence alignments for sequence similarity analyses.