Systomics Network
Sub-HMM Viewer
UC Riverside
   Sub-HMM Viewer   |   Cluster Display   |   Downloads   

This page can be used to display a specific sub-HMM, all the sub-HMMs of a certain family, or all the sub-HMMs in a certain cluster. A list of families can be found here

To list all sub-HMMs for a family, leave the 'Sub HMM' box blank and click the search button. To list a specific sub-HMM, enter the family name in the 'Family' box, and the sub-HMM number in the 'Sub-HMM' box, then click search. To list other members of the cluster, specify both the family name and the sub-hmm id, then use the cluster button. See the cluster list for more details on the clustering.

If you are viewing a cluster of Sub-HMMs, you can view the alignment of each sub-HMM with another sub-HMM by using the links in the table below the logo. Not all alignment methods work, so some of the links below will return an error page. The score of the local-local alignment is also given, with 0 being the best (closest) score and higher scores being worse. Alignments are done with PRC.

You can view a list of all clusters here: Cluster list

'Family' should be the name of a PFAM family, with or without a version extention. E.g.: PF00004.20 or PF00004. 'Sub-HMM' should be the number of the Sub-HMM.

A sub-HMM is subset of a full HMM. In this case, we used HMMs from PFAM families. For each full HMM, we extract several sub-HMMs which capture the most important parts of the full HMM.

You can search our sub-HMMs using our search page.

Family: Sub HMM:

Sequence Search

   Thomas Girke, UC Riverside, Email: thomas.girke@ucr.edu