Quality control strategies can be used to increase accuracy of and confidence in results from gene finding tools. First, the abundance of repetitive elements in genomic sequences can distort predictions of genes and exon locations. To counter this problem, masking genomic sequences is recommended, before gene analysis, using a program like RepeatMasker (A.F. A. Smit et al. 1996, unpublished) . The effectiveness of Repeat-Masker with marine and other evolutionarily divergent organisms is not yet clear because interspersed repeats are specific to a species or group of species. Sequences from such organisms should be evaluated under masked and unmasked conditions. Second, aligning ESTs or cDNAs with genomic sequences using programs like Spidey (http://www.ncbi.nlm.nih.gov/spidey/; Wheelan et al. 2001 ) refines predictions of exon and intron boundaries, promoter regions, and splice sites. This approach presents challenges for transcripts that are expressed at very low levels, have significant tissue-or age-specific requirements, or are from species for which minimal sequencing has been done (Schwartz et al. 2000) . A new, publicly available resource, the Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org; Mattingly et al. 2003 Mattingly et al. , 2004a , provides multiple alignment and phylogenetic analysis results with sequences from diverse organisms for biomedically significant genes and proteins. CTD provides access to data valuable for identifying homologous genomic sequences and confirming gene and gene feature predictions. Identification of gene features greatly improves interpretation of subsequent multiple sequence analysis results.