The projects contain details concerning a specific sequencing effort, such as its type (genomic DNA or EST/cDNA) and a link to the web-page providing the primary data. Projects can be selected based on the sequence data available for the species. Thus, species might be selected for which only cDNA/EST data or only genomic data is available, or those for which both cDNA/EST and genomic data is available. The term completeness is intended to describe the coverage of the genome and the chance to find all homologs of the gene of interest. For detailed information have a look at the FAQ's pages. The completeness option offers the possibility to search for those species for which the chance to find all homologs (and complete genes) to the protein of interest is very high. Projects can also be selected based on several services provided, like BLASTP or TBLATN.
The genome assemblies release option is a nice tool to select those genomes that have been finished in a certain time scale. Thus, the history of the genome sequencing efforts can be analysed (of course with limitations).
The projects have been organized by references, a term we use for the large-scale sequencing centers (e.g. the DOE Joint Genome Insitute) or community species homepages (e.g. FlyBase). By choosing references it is possible to search for the output of a single or more sequencing centers. However, for many species, the sequence information is not available via a dedicated species home page but only via GenBank. Therefore the "GenBank" links (associated to the GenBank reference) of the species projects provide BLAST search forms including the corresponding database (some data is only available from the WGS, other from the EST database) and the corresponding species name.