CIPRO 2.5

CIPRO 2.5 provides an integrated protein sequence and annotation resource for the tunicate Ciona intestinalis to support developmental and evolutionary biology research.

Key Features:

• Phylogenetic significance: Ciona intestinalis occupies an important phylogenetic position as a tunicate, enabling comparative studies relevant to vertebrate evolution.
• Extensive data collection: Aggregates published literature and unpublished experimental data including large-scale transcriptomic and proteomic datasets.
• Diverse data types: Integrates 3D expression profiling, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and mass spectrometry-based analyses.
• Comprehensive sequence coverage: Built on a KH model containing 36,034 unique sequences and encompassing 89,683 known and predicted proteins from all Ciona intestinalis gene models, with over 10,000 proteins manually annotated.
• Homologous information: Includes homologs in humans and other major model organisms to support cross-species comparisons and functional inference.
• Community annotation: Incorporates community evaluation and annotation of protein entries to refine and expand curated information.

Scientific Applications:

• Developmental biology: Supports analysis of gene expression patterns, protein functions, and morphological development in Ciona intestinalis.
• Comparative and evolutionary studies: Enables comparative analyses across species to investigate genetic underpinnings of vertebrate evolution using sequence and homolog data.
• Proteomics and functional annotation: Facilitates proteomic investigations and functional annotation through integrated 2D-PAGE, mass spectrometry data, and curated annotations.

Methodology:

Constructed from published literature, unpublished experimental data, and curated annotations, and employing bioinformatics techniques to integrate diverse transcriptomic, proteomic, expression profiling, and sequence datasets.