Pfaat Daniel Caffrey, Paul Dana, Enoch Huang Research Technology Center Cambridge MA USA pfaat.sourceforge/

1. d Pfaat Daniel Caffrey, Paul Dana, Enoch Huang Research Technology Center Cambridge MA USA http://pfaat.sourceforge.net/ Annotate Residues Summary. PFAAT is a JAVA based application designed to facilitate the analysis and annotation of large protein families. Since its release in 2003, a number of feature enhancements have been added: 1). Improved synchronization and selection between alignment sequences, tree nodes, and structural elements. 2). Sequence annotation now includes 10 synonyms, a user defined web link, and an unlimited number of user defined annotations. 3). Sequences can be sorted and filtered by residue composition in a column, sequence name, and percent identity. 4). A number of published residue properties are available for the analysis of binding sites. 5). Novel algorithms to analyze sequence conservation. 6). Cluster Ids can be assigned via a vertical bar on the tree viewer. 7) Tree branches can be colored by cluster ID, sequence annotation, and user designation. • View Structures with JMOL • Select residues in alignment and structure • Coming soon.. Map residue conservation to structure Menus in Alignment Viewer Correlate Compute correlation coefficient between sequence annotation (e.g. substrate affinity) and residue properties for each column (e.g. volume). • Line Annotation • Annotate secondary structure and domain boundaries • Tree Viewer • New features added to ATV • Select sequences in tree and alignment • Access sequence annotations on nodes • Define cluster ID with vertical bar • Color branches by cluster ID, user definition • Numbering • Sequence • Alignment column • Residue index • User defined number • Number of reference sequence • Filter / Sort • Filter or sort sequences based on selected residue • Display residue frequencies in a column • Annotate Sequences • Synonyms • substrate affinity • URL and link button to launch browser • Species • Cluster ID from tree • Display Consensus • View highly conserved or similar columns in alignment with von Neumann entropy and other conservation scores • References • Jason M. Johnson, Keith Mason, Ciamac Moallemi, Hualin Xi, Shyamal Somaroo, and Enoch S. Huang. Bioinformatics 2003 Mar;19(4):544-545 • www.jmol.org • http://pfaat.sourceforge.net The icons are trademarks of the associated companies