SUPERFAMILY 1.75 HMM library and genome assignments server

How to View Genome Assignments

To view genome assignments you must choose a superfamily for which you would like to view the assignments. This can be done in four ways:

  • Choose a genome first, then follow a link to the assignments for the superfamily from a list.

  • 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 genome assignments 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 assignments for that superfamily. You can also follow the link to the alignment page where you can view alignments of genome sequences to your query sequence.

  • Browse through the SCOP hierarchy until you find your superfamily of interest. Then follow the Genome Assignments link.

The assignments are produced by scoring all genomes against the HMM library. The assignment procedure then compares all matches made to all regions of sequences. Where more than one hit is made to the same region, the one with the highest score is chosen. In this way structural domains are assigned to genome sequences, and hence something about their function may be inferred.

Some degree of human intervention and effort goes into improving these assignments to try to make them the best possible.