CCT

CCT performs automated and customized searches of remote sequence and hidden Markov model (HMM) databases to support gene and ortholog identification and to track sequence and annotation changes.

Key Features:

• Automated and customizable searches: Executes automated and user-customizable search workflows against remote sequence and HMM databases.
• Support for search programs: Integrates BLAST and hmmpfam for sequence- and HMM-based similarity searches.
• BioPerl core: Utilizes a BioPerl core for sequence-data parsing and workflow integration.
• Result aging and annotation tracking: Color-codes result files based on age and highlights minor sequence or annotation changes for comparative assessment.
• Database submission and batch analysis: Facilitates rapid database submissions and subsequent automated analysis of returned results.

Scientific Applications:

• Gene and ortholog identification: Identifies candidate genes and orthologs through sequence- and HMM-based searches.
• Comparative sequence monitoring: Detects and highlights minor sequence and annotation changes across result sets and over time.
• Large-scale molecular dataset analysis: Enables processing of extensive molecular datasets via automated, batchable searches and analyses.

Methodology:

Uses a BioPerl core, executes BLAST and hmmpfam searches against remote sequence and HMM databases, produces color-coded result files that flag sequence/annotation differences, and supports automated database submissions for downstream analysis.