Due to the existence of several protein identifier types (FM3.1, FM4, Au5, Au10.2), different identifiers are associated with an individual protein within the Chlamydomonas genome. In order to extend annotations from one identifier type to another, matching protein identifiers are deduced by sequence similarity filtering for mutual best hits between identifiers using BLAST. Matching identifiers with 100% sequence coverage are kept, and the rest of the mutual best hits are filtered to include only those proteins with matches with at least 75% coverage. Potential ambiguities involving proteins similar to multiple other proteins are resolved by considering only the reciprocal best hit from the BLAST query in the opposite direction. The information derived by this analysis is used to convert gene identifiers between different types, which allows the Algal Annotation Tool to work with multiple protein identifier types.