d-Omix: a mixer of generic protein domain analysis tools

DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins

DoMosaics is an application that unifies protein domain annotation, domain arrangement analysis and visualization in a single tool. It simplifies the analysis of protein families by consolidating disjunct procedures based on often inconvenient command-line applications and complex analysis tools. It provides a simple user interface with access to domain annotation services such as InterProScan or a local HMMER installation, and can be used to compare, analyze and visualize the evolution of domain architectures.

AVAILABILITY AND IMPLEMENTATION

DoMosaics is licensed under theApache License, Version 2.0, and binaries can be freely obtained from www.domosaics.net.

An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins

Annotations of the genes and their products are largely guided by inferring homology. Sequence similarity is the primary measure used for annotation purpose however, the domain content and order were given less importance albeit the fact that domain insertion, deletion, positional changes can bring in functional varieties. Of late, several methods developed quantify domain architecture similarity depending on alignments of their sequences and are focused on only homologous proteins. We present an alignment-free domain architecture-similarity search (ADASS) algorithm that identifies proteins that share very poor sequence similarity yet having similar domain architectures. We introduce a “singlet matching-triplet comparison” method in ADASS, wherein triplet of domains is compared with other triplets in a pair-wise comparison of two domain architectures. Different events in the triplet comparison are scored as per a scoring scheme and an average pairwise distance score (Domain Architecture Distance score - DAD Score) is calculated between protein domains architectures. We use domain architectures of a selected domain termed as centric domain and cluster them based on DAD score. The algorithm has high Positive Prediction Value (PPV) with respect to the clustering of the sequences of selected domain architectures. A comparison of domain architecture based dendrograms using ADASS method and an existing method revealed that ADASS can classify proteins depending on the extent of domain architecture level similarity. ADASS is more relevant in cases of proteins with tiny domains having little contribution to the overall sequence similarity but contributing significantly to the overall function.