Figure 2

PhyloFacts search results for ANDR_RAT, androgen receptor from Rattus norvegicus. Books with significant scores are displayed graphically at top, followed by various statistics about each match in a table below. The top-scoring book (red bar) represents a global homology group of Androgen receptors, which matches the entire query sequence. Examining the table below shows the Androgen receptor book has an E-value of 2.71e-162, 91% identity between the query and book consensus (based on aligned residues), and high fractional coverage of the HMM (99%). Other global homology groups retrieved include evolutionarily related Glucocorticoid and Progesterone receptors, but analysis of query coverage and percent identity shows the Androgen receptor book to provide a superior basis for annotation transfer. Other books displayed include structural domains detected in the query. Two books (for the ligand-binding domain 1kv6a and the DNA-binding domain 1dsza) were constructed for the Structure Prediction series based on SCOP domains. Subsequent construction of the specialized book series on transmembrane receptors in the human genome resulted in additional books being constructed for these domains. Scoring subfamily HMMs is enabled by selecting the 'Search subfamilies' box (second column in the spreadsheet of results, shown checked in the figure), and clicking on the 'Go' button at bottom ('Search selected books for top-scoring subfamily HMMs against query'). Clicking on the 'Go' button below 'View alignment' in the first column brings up a separate page displaying the pairwise alignment of the query and the family consensus sequence along with relevant statistics about the alignment. Clicking on the hyperlink to the book itself (in the 'PhyloFacts book' column) retrieves the webpage for the family (see example book page shown in Figure 1).