Scheduled Seminars on 11/4/2010

DEWEESE SCOTT CAROL at 11:00  Edit  Reschedule  Delete

Conserved Domain Database (CDD): The Challenge and Importance of Producing Accurate Sequence Alignments
The Conserved Domain Database (CDD) is a collection of models representing ancient conserved domains, organized into family/superfamily hierarchies based on the sequence alignments of the member proteins. As such, the generation of accurate multiple sequence alignments is a vital part of the CDD curation process. In most protein families, certain features and conservation patterns can be easily identified, but other regions of the protein sequence are much less homologous. In these cases, generating good sequence alignment models can be very challenging. The CDD curation team utilizes two software packages (CDTree and Cn3D) developed by members of the Structure team, working closely with the CDD curators. These extremely useful applications are regularly updated to include new features/capabilities that allow users more ease and accuracy in generating multiple sequence alignments. The challenges and importance of producing accurate multiple sequence alignments will be discussed, and several of the CDTree and Cn3D techniques used in the curation process will be demonstrated.


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