Protein family analysis at the domain-level

The analysis of protein domains has gained considerable attention over the last years. Many new insights on protein modular evolution, combined with improved domain detection, have paved the way for an integrated analysis of protein families from a domain-centric perspective. We recently released DoMosaics, a JAVA application that facilitates the interactive analysis of protein domain arrangements. DoMosaics combines guided domain annotation, a highly-customisable visualization of arrangements, and a number of analysis tools. It also integrates domain-centric algorithms such as CODD, which is used for the detection of divergent domain occurences that have escaped Pfam thresholds, as well as RADS/RAMPAGE which provides means to search for proteins with a domain arrangement similar to a given query. RADS provides an alignment of domain strings as opposed to amino-acid sequences, while RAMPAGE produces an amino-acid alignment guided by RADS results. Hence, RADS/RAMPAGE produces fast and yet accurate alignments, and associated ranking, of proteins with similar domain arrangements. Together, these tools greatly simplify the domain-centric analysis of protein function, structure and evolution.