The Trans-NIH Zebrafish Genome Initiative at Children's Hospital Boston aims to annotate zebrafish genes with human known genes for functional and comparative studies. This website provides a web service for retrieving annotated zebrafish genes represented on Affymetrix Zebrafish Genome Arrays and Roche-NimbleGen Zebrafish Expression Arrays to the research community. We have combined automated and manual annotation processes to create the orthology. The automated annotation phase used algorithms to rapidly analyze thousands of BLAST HSPs and make orthology calls. The manual annotation phase required hand-examination of each BLAST result to make orthology calls by scientists in the Zon Lab using a web-interface developed in-house. Researchers can choose to download the entire annotation as a text file, or retrieve their specific gene probesets of interest by submitting a list of probe IDs of interest. A key word search function is added to retrieve gene annotation by key words used in gene names and descriptions. We are now annotating all zebrafish genes including genes represented on zebrafish expression array platforms. The output file of this project will contain gene names, their corresponding genome locations, and probe IDs on different arrays. We will continue annotating as new sequence data become available and by comparative genomics approaches.