Nucleic Acids Research, 2009, Vol. 37, Web Server issue W555 Table 1. Examples of motifs found for an interested protein (UniProt entry P35835) Motif sources MAGIIC-PRO GLAM2 PROSITE PROSITE PROSITE ELM ELM Motifs H-G-T-x(3)-G-x(77,101)-A-x-G-N-x(57,78)-G-T-S-x(3)-P 165-214 or QDGSSHGTHVAGTIAALNNSIGVLGVAPSASLYAVKVLDSTGSGQYSWII [STAIV]-{ERDL}-[LIVMF]-[LIVM]-D-[DSTA]-G-[LIVMFC]-x(2,3)-[DNH] H-G-[STM]-x-[VIC]-[STAGC]-[GS]-x-[LIVMA]-[STAGCLV]-[SAGM] G-T-S-x-[SA]-x-P-x-{L}-[STAVC]-[AG] [RK].[AILMFV][LTKF] Y[QDEVAIL][DENPYHI][IPVGAHS] Database ID PS00136 PS00137 PS00138 CLV_PCSK_SKI1_1 LIG_SH2_SRC overlap on the reference sequence are assigned with the same color to show their relationships. On the other hand, a block without overlapping with the others can be col- ored in two ways: (i) the simpler one—blocks belonging to the same motif have a single color; (ii) the more complex one—each of the blocks has its own color. In single-motif mode, the adopted coloring scheme is simple. Each motif takes a distinct color, and for the selected motif all the matched positions are shown simultaneously. Multi-block motifs are excluded from the list, since it would be too complicated to show all the occurrences at the same time. The matched residues on the collected PDB chains are colored in agreement with the reference sequence to show their correspondences. Once the visualization method is selected, seeMotif generates a list of the col- lected protein structures for selection and equips a Jmol plug-in (available at http://www.jmol.org/) for rendering the selected protein structure. In addition, the domain information from Pfam is considered for further ﬁltering unwanted matches. When users decide to see only motifs outside a domain, blocks having any positions inside a domain are excluded. Conversely, when users decide to see only motifs inside a domain, only blocks having all positions inside a domain are reserved. Users can just turn oﬀ this ﬁlter by selecting the option ‘both are ﬁne’. Screenshots and more detailed explanations of how to use these facilities for exploring and visualizing motifs can be found in the following section. EXAMPLES With a sequence of interest, researchers can conduct motif discovery through motif discovery web servers or standalone command-line tools. Usually a set of homolo- gous sequences of the query protein is required during motif discovery process. This is often achieved by per- forming sequence alignment tools against existing sequence databases like UniProt. Alternatively, some motif discovery servers ask for the sequence set for com- putation directly from the users. In addition to ﬁnding potential motifs from scratch, users also frequently exploit pattern matching utilities provided by curated motif data- bases such as PROSITE and ELM. In this section, we use the protein Subtilisin NAT of Bacillus (UniProt entry P35835) as an example to demonstrate what seeMotif can do with the sequence motifs discovered by computa- tional tools or extracted from motif databases described above. In Table 1, we show seven sequence motifs, two discov- ered by mining algorithms and ﬁve from databases. seeMotif accepts patterns of diﬀerent styles in a single query. We can send a query by using a combination of the three-block motif from MAGIIC-PRO along with the polypeptide QDGSSHGTHVAGTIAALNNSIGVLGVA PSASLYAVKVLDSTGSGQYSWII that GLAM2 (35) reports as the region of the best motif it found. This one-block motif can be speciﬁed alternatively by its range on the reference sequence, 165–214. It is shown in Figure 1 that both the ﬁrst block of the ﬁrst motif and the second motif match the segment ‘HGTHVAG’ of the reference sequence. Namely, these two blocks are overlap- ping. This is why they share the same color in multi-motif visualization mode. As shown in the structure view embedded in Figure 1, all the motif blocks used are related to the catalytic site, though some position mutations are observed in the longest block (area marked with the number ‘5’ in Figure 1). There are more than 100 struc- tures found in PDB for this query. Each contains at least one protein chain homologous to the reference sequence. A sequence alignment view showing the correspondences between the reference sequence and the collected PDB chains can be found by clicking an external link, named ‘sequence alignment’, provided above the structure panel. Next, we attempt to examine more patterns listed in Table 1 in a single run of seeMotif, where the three PROSITE patterns can be quickly speciﬁed by using PROSITE IDs PS00136, PS00137 and PS00138. In the intermediate page, it is warned that only up to ﬁve motifs can be visualized in a single run owing to perfor- mance consideration. We unselected the PROSITE pat- tern PS00136, added the ELM motif ‘LIG_SH2_SRC’ and then submitted the query (subﬁgure marked with the number ‘5’). When visualizing the motifs in multi- motif mode, overlapping motif blocks are plotted in the same colors. In this example, as shown in Figure 2 (area marked with the number ‘2’), two combinations of posi- tion mappings are identiﬁed by seeMotif for multi-motif mode. These two mapping possibilities are owing to the multiple matches of the short motif from ELM data- base, ‘Y[QDEVAIL][DENPYHI][IPVGAHS]’. Once the mapping combination is changed, all the motifs will be re-mapped on the reference sequence as well as in the structure panel. In the structure panel, structures are by default sorted by the e-values reported from execution of BLAST. seeMotif provides three additional strategies to reorder the structure list. If the users are interested in knowing whether the motifs play an important role