Iccare

Iccare performs annotation and comparative mapping of expressed sequence tags (ESTs) and mRNA sequences to compare query organisms to the transcriptomes of Homo sapiens and Arabidopsis thaliana.

Key Features:

• Input data: Leverages EST and mRNA sequences from public databases for the query species.
• Reference transcriptomes: Compares query sequences against the transcriptome gene sets of Homo sapiens or Arabidopsis thaliana.
• Comparative mapping: Systematically compares query ESTs/mRNAs to reference transcriptomes to map relationships between sequences.
• Graphical representation: Produces graphical outputs that align comparative results with chromosomal locations of genes in the reference organism.
• Integration of gene structure and similarity: Combines gene structure information and sequence similarity data into unified visualizations.
• Annotation and characterization: Identifies the nature of query transcript sequences through similarity to known genes in the reference genome.
• Primer/probe design: Enables design of primers or probes for physical or genetic mapping experiments based on comparative results.
• Custom sequence search: Accepts user-provided sequences for tailored comparative analysis against reference gene sets.

Scientific Applications:

• Comparative genomics: Comparative mapping between a query organism and Homo sapiens or Arabidopsis thaliana transcriptomes to study conservation and divergence.
• EST and transcript annotation: Annotation and classification of ESTs and mRNAs by similarity to reference genes.
• Evo-devo and evolutionary studies: Identification of conserved genes and assessment of evolutionary relationships between species.
• Functional genomics: Support for investigating gene conservation and putative function via mapped homologs.
• Experimental design: Generation of primers or probes to enable physical or genetic mapping and experimental validation of computational predictions.

Methodology:

Retrieves EST and mRNA sequences from public databases, compares them against the transcriptome gene sets of Homo sapiens or Arabidopsis thaliana, integrates gene structure and sequence similarity information into graphical representations aligned to chromosomal locations, supports primer/probe design, and accepts user-provided sequences for tailored comparisons.