As with all tools that integrate data from multiple external sources, the power of analysis using the Algal Functional Annotation Tool is ultimately limited by the quality of the annotations within the primary databases. With the steady growth of knowledge in these annotation databases, the utility of the analyses provided is expected to increase in the future as more biologi­cal associations are assigned to genes. Additionally, as Chlamydomonas rein­hardtii genes continue to be experimentally characterized, the assignment of manual annotations will also fill in the gaps left by automated annotation as­signment and thus expand the annotation coverage throughout the genome, further improving the results generated by our portal. Lastly, the extensible nature of the Algal Functional Annotation Tool will allow us to add other algal organisms in the future using the same platform so that genomic data from other algal model organisms may be analyzed in a similar fashion as that currently available for Chlamydomonas reinhardtii.

11.3 CONCLUSIONS

The Algal Functional Annotation Tool is intended as a comprehensive analysis tool to elucidate biological meaning from gene lists derived from high-throughput experimental techniques. Annotation sets from a num­ber of biological databases have been pre-processed and assigned to gene identifiers of the green alga Chlamydomonas reinhardtii, and this annotation data may be explored in multiple ways, including the use of enrichment tests designed for large gene lists. Furthermore, the site enables the visu­alization of proteins within pathway maps. Using several methods, such as inferring annotations from orthologous proteins of other organisms, the initially sparse annotation coverage of C. reinhardtii is alleviated, allowing for a more effective functional term enrichment analysis. Other functions of the tool include a batch gene identifier conversion tool and a manual annotation search tool. Lastly, similar genes based on expression across several conditions may be explored using the gene similarity search tool.

11.4 AVAILABILITY AND REQUIREMENTS

• Project name: Algal Functional Annotation Tool

• Public web service: http://pathways. mcdb. ucla. edu webcite; Free and no registration.

• Programming language: Perl/CGI

• Database: MySQL

• Software License: GNU General Public License