KARMA

KARMA facilitates comparison and annotation of user-defined microarray platforms across single or multiple species for comparative and functional genomic analyses.

Key Features:

• Cross-Species Comparison: Supports within-species comparisons using NCBI-Unigene identifiers and between-species analyses using NCBI-Homologene to identify analogous DNA fragments.
• Platform Versatility: Accepts arrays from the Keck Microarray Resource at Yale, Affymetrix GeneChips, spotted arrays, and custom researcher arrays.
• Dynamic Data Input: Accepts pairs of test files representing different array platforms to enable comparisons of single- or multiple-species datasets.
• Comprehensive Annotation: Integrates annotation from LocusLink, SwissProt, and Gene Ontology (GO), dynamically retrieving data from remote sites and storing annotations in an Oracle database.
• Set Operations for Analysis: Implements set operations (intersection, union, difference) for single-species comparisons.
• Regular Updates: Maintains periodic updates of the KARMA database to include current annotation data.

Scientific Applications:

• Comparative Genomics: Enables cross-platform and cross-species identification of conserved genetic elements using NCBI-Unigene and NCBI-Homologene mappings.
• Functional Genomics: Supports gene function annotation and interpretation of microarray expression data using integrated LocusLink, SwissProt, and GO annotations.
• Systems Biology: Facilitates integration of annotated expression data to support systems-level analyses of biological processes.

Methodology:

Collects genome annotation data from multiple sources; dynamically identifies analogous DNA fragments using NCBI-Unigene and NCBI-Homologene identifiers; performs set operations (intersection, union, difference) for single-species comparisons; dynamically retrieves annotation data from remote sites and stores integrated annotations in an Oracle database; database is periodically updated.