Explore characteristics of amino acids by comparing their structural and chemical properties, predicting protein sequence changes caused by mutations, viewing common substitutions, and browsing functions of given residues in conserved domains.
A stand-alone application for classifying protein sequences and investigating their evolutionary relationships. CDTree can import, analyze and update existing Conserved Domain (CDD) records and hierarchies, and also allows users to create their own.
COBALT is a protein multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST.
The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations.
Available information includes: Announcements, Overview, Access and Availability, Collaborators, CCDS Identifiers and Tracking, Process Flow and Quality Testing, Publications.
Initial results from the Consensus CDS project are now available from the participants' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records. CCDS reports can be accessed by following provided links, or by directly querying the underlying database using the query interface provided at the top of the home page. The CCDS dataset is also available for anonymous FTP.
An interactive Web application that enables users to visualize multiple alignments created by database search results or other software applications. The MSA Viewer allows users to upload an alignment and set a master sequence and to explore the data using features such as zooming and changing of coloration.
A utility for computing alignment of proteins to genomic nucleotide sequence based on a variation of the Needleman Wunsch global alignment algorithm and specifically accounts for introns and splice signals.
A computer algorithm that identifies similar protein 3-dimensional structures. Structure neighbors for every structure in MMDB are pre-computed and accessible via links on the MMDB Structure Summary pages.