SUPERFAMILY Alignments

To view alignments you must first choose a superfamily for which you would like to view the alignments. This can be done in three ways:

• Go to the search page and enter keywords or PDB identifiers, this should take you to the correct superfamily. From there follow the link to the alignments for the selected superfamily.

• Enter a sequence for searching against the HMM library. The sequence will be assigned a superfamily, you can then follow the link to the alignments for that superfamily.

• Begin by choosing a genome from the list on the genomes page then select a superfamily belonging to your chosen genome. From the assignments page you will have the option to click on 'ALIGN' and view the sequences belonging to that superfamily in that genome which you have selected.

Once you have reached the alignment page you must choose sequences to add to the alignment, as the default is that a single example sequence is shown aligned to the model.

The most important thing to realise about the alignments is that what you see are sequences aligned to a model. The model is not displayed, but the segment numbers of the model nodes are shown. As a consequence it is not a true multiple alignment, and if many sequences are added to the alignment it may appear fragmented even if each individual sequence is well aligned to the model. In this case display fewer sequences in the alignment.