W446 Nucleic Acids Research, 2007, Vol. 35, Web Server issue Figure 1. Outlook of the application pages for the pipeline analyses. (ii) Identiﬁed Protein and Transcripts, (iii) Features and Functions, (iv) Genomic Localisation and (v) Homology to Other Organisms/Genes. The information provided in each of these sections is provided in Figure 2 and Supplementary Table 2. The user has immediate access to all complete application outputs and database entries via hyperlinks. At the bottom of the HTML output there is a link to the explanatory legend as well as to the XML output containing all the generated information. DomainSweep identiﬁes the domain architecture within a protein sequence and therefore aids in ﬁnding correct functional assignments for uncharacterized protein sequences (Figure 3). It employs diﬀerent database search methods to scan a number of protein/domain family databases. Among these models, in increasing complexity, are: PRODOM (10), automatically generated protein family consensus sequences, PROSITE (11) regular-expression patterns, BLOCKS (12), ungapped position-speciﬁc scoring matrices of sequence segments, PRINTS (13) sequence motifs, PROSITE proﬁles (7), gapped position-speciﬁc scoring matrices and Hidden Markov Models like PFAM (14), SMART (15), TIGRFAMS (16) and SCOP (17). Each database covers a slightly diﬀerent, but overlapping set of protein families/ domains. Each model has its own diagnostic strengths and weaknesses and for each of these protein/domain family databases used we have established diﬀerent thresholds. For example, in the case of the database PFAM-A, we compare the input sequence against the Hidden Markov model proﬁle of each PFAM protein family.