BMC Genomics 2006, 7:116 http://www.biomedcentral.com/1471-2164/7/116 FGiegnueren3try for one transcript Gene entry for one transcript. Complete gene description for one transcript, ENSANGT00000011456. Each entry displays the developmental expression profile built for the transcript from stage- and tissue-specific microarray analyses, followed by a link to Vectorbase and functional annotation gathered by Ano-Xcel [5] from the ENSEMBL, NCBI non-redundant, PFAM, GO, and SMART databases. The bottom of each entry includes user-contributed notes if they are available, as well as a form for users to submit their own notes for immediate listing. Each link in the matrix invokes a new page that prints the promoter sequences of the two genes being compared with areas of sequence conservation and transcription fac- tor binding sites highlighted (Figure 5). Second, a table of the conserved motifs is displayed that compares the fre- quency of occurrence of each conserved motif within the gene set against the frequency of each motif in all 1) exons, 2) exons and introns, and 3) promoters within the An. gambiae genome (Figure 6). Each motif that matches or contains a transcription factor binding site is indicated in the same output. The third item displayed is a table indicating the frequency of occurrence of each transcrip- tion factor binding site of any size found within the gene set (Figure 7). Due to the degeneracy and varied size of transcription factor binding sites in the TFD database, the frequencies reported here are noticeably higher in this item compared to the frequencies in the conserved motif table that precedes it. PFrigoumroete4r comparison matrix Promoter comparison matrix. Each transcript in the current gene set is displayed in a matrix indicating the number of con- served motifs found between each transcript when compared pair-wise with every other transcript within the gene set. The matrix shown corresponds to the prophenoloxidase case study gene set, with the promoter regions of the six transcripts being compared to search for conserved DNA sequence motifs that are 12 nucleotides in length, with no mismatched bases allowed. Each link in the matrix invokes the sequence comparison output shown in Figure 5. Page 4 of 11 (page number not for citation purposes)